Parthenogenic activation of human oocytes for the production of human embryonic stem cells

ABSTRACT

Methods of producing human stem cells are disclosed for parthenogenetically activating human oocytes by manipulation of O2 tension, including manipulation of Ca2+ under high O2 tension and contacting oocytes with serine threonine kinase inhibitors under low O2 tension, isolating inner cell masses (ICMs) from the activated oocytes, and culturing the cells of the isolated ICMs under high O2 tension. Moreover, methods are described for the production of stems cells from activated oocytes in the absence of non-human animal products, including the use of human feeder cells/products for culturing ICM/stem cells. Stem cells produced by the disclosed methods are also described.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser. No. 14/945,326 filed Nov. 18, 2015, now issued as U.S. Pat. No. 11,324,778; which is a divisional application of U.S. application Ser. No. 12/759,654 filed Apr. 13, 2010, now abandoned; which is a divisional application of U.S. application Ser. No. 11/505,260 filed Aug. 15, 2006, now issued as U.S. Pat. No. 7,732,202; which claims the benefit under 35 USC § 119(e) to U.S. Application Ser. No. 60/813,799 filed Jun. 14, 2006; U.S. Application Ser. No. 60/758,443 filed Jan. 11, 2006; U.S. Application Ser. No. 60/733,309 filed Nov. 2, 2005; and to U.S. Application Ser. No. 60/729,177 filed Oct. 21, 2005, all now expired. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The material in the accompanying sequence listing is hereby incorporated by reference into this application. The accompanying sequence listing text file, named ISCC1110-8_ST25.txt, was created on May 6, 2022 and is 5 kB in size. The file can be accessed using Microsoft Word on a computer that uses Windows OS.

BACKGROUND OF THE INVENTION Field of the Invention

The present invention relates generally to embryonic stems cells, and more specifically, to a process for obtaining human embryonic stem cells using parthenogenically activated oocytes.

Background Information

Human embryonic stem cells (ES) cells are pluripotent cells that can differentiate into a large array of cell types. When injected into immune-deficient mice, embryonic stem cells form differentiated tumors (teratomas). However, embryonic stem cells that are induced in vitro to form embryoid bodies (EBs) provide a source of embryonic stem cell lines that are amenable to differentiation into multiple cell types characteristic of several tissues under certain growth conditions. For example, ES cells become differentiated into neurons in the presence of nerve growth factor and retinoic acid.

Human ES cells and their differentiated progeny are important sources of normal human cells for therapeutic transplantation and for drug testing and development. Required by both of these goals is the provision of sufficient cells that are differentiated into tissue types suitable for a patient's needs or the appropriate pharmacological test. Associated with this is a need for an efficient and reliable method of producing differentiated cells from embryonic stem cells.

Currently, human embryonic stem cells (hES) are derived from three sources: blastocysts remaining after infertility treatments and donated for research, blastocysts generated from donated gametes (oocytes and sperm), and the products of nuclear transfer (NT). Cadaveric fetal tissue is the only source of human embryonic germ cells (hEG). hES and hEG cells offer remarkable scientific and therapeutic possibilities, involving potential for generating more specialized cells or tissues. Ethical concerns about the sources of hES and hEG cells, however, and fears that use of NT for research could lead to use of NT to produce a human being, have fostered a great deal of public discussion and debate.

Parthenogenic activation of mammalian oocytes may be used as an alterative to fertilization by sperm/NT to prepare oocytes for embryonic stem cell generation. Parthenogenic activation is the production of embryonic cells, with or without eventual development into an adult, from a female gamete in the absence of any contribution from a male gamete.

Parthenogenetic activation of mammalian oocytes has been induced in a number of ways. Using an electrical stimulus to induce activation is of particular interest because electrofusion is part of the current nuclear transfer procedure. Parthenogenetic activation in vitro by electrical stimulation with electrofusion apparatus used for embryonic cell-oocyte membrane fusion has been reported.

Mouse oocytes have been activated by exposure to Ca⁺²—Mg⁺² free medium, medium containing hyaluronidase, exposure to ethanol, Ca⁺² ionophores or chelators, inhibitors of protein synthesis, and electrical stimulation. These procedures have led to high rates of parthenogenic activation and development of mouse oocytes, but did not activate and/or lead to a lower development rate of young bovine oocytes. Further, fertilization and parthenogenic activation of mouse oocytes is also dependent on post ovulatory aging.

Activation of bovine oocytes has been reported by ethanol, electrical stimulation, exposure to room temperature, and a combination of electrical stimulation and protein inhibition with cycloheximide. While these processes are thought to raise intracellular Ca⁺², they are most successful when the oocytes have been aged for more than 28 hours.

SUMMARY OF THE INVENTION

The present invention is based on the seminal discovery that certain conditions are optimal for parthenogenically activating human oocytes.

In one embodiment, a method of producing human stem cells is provided including parthenogenetically activating an oocyte, where activation includes contacting the oocyte with an ionophore at high oxygen (O₂) tension and contacting the oocyte with a serine-threonine kinase inhibitor under low O₂ tension, cultivating the activated oocyte at low O₂ tension until blastocyst formation, transferring the blastocyst to a layer of feeder cells, and culturing the transferred blastocyst under high O₂ tension, mechanically isolating an inner cell mass (ICM) from trophectoderm of the blastocyst, and culturing the cells of the ICM on a layer of feeder cells, where culturing the ICM cells is carried out under high O₂ tension. Preferably, the oocyte is human.

In a related aspect, low O₂ tension is maintained by incubation in a gas mixture environment comprising an O₂ concentration of about 2% O₂ to about 5% 02, where the gas mixture environment further comprises about 5% CO₂ and about 90% nitrogen (N₂) to 93% N₂.

In another embodiment, a method of activating human metaphase II oocytes is provided including incubating human metaphase II oocytes in in vitro fertilization (IVF) media under high O₂ tension, activating by incubating the cells in IVF media comprising an ionophore under high O₂ tension, and subsequently incubating the cells in IVF media comprising a serine-threonine kinase inhibitor (STKI) under low O₂ tension, and incubating the STKI treated cells until blastocyst formation under low O₂ tension, where inner cell masses (ICM) obtained from the blastocyst produce culturable stem cells. High O₂ tension may be maintained by incubating the cells in a gas mixture environment having about 5% CO₂, about 20% 02, and about 75% N₂.

In a related aspect, the O₂ tension for the incubating steps subsequent to activation is maintained by incubating the cells in a gas mixture environment comprising an O₂ concentration of about 2% O₂ to about 5% 02, where the gas mixture environment further includes about 5% CO₂ and about 90% N₂ to about 93% N₂.

In another related aspect, the IVF media is essentially free of non-human products.

In a further related aspect, isolated oocytes prepared by the invention methods are provided, including isolated inner cell masses (ICM) prepared from such oocytes and corresponding stem cells isolated therefrom.

In another embodiment, human parthenogenic activation of mammalian oocytes resulting in embryogenic stem cells and their differentiated progeny is provided. Such cells and progeny are substantially isogenic to the oocyte donor, thus allowing for autologous transplantation of cells relative to the oocyte donor, and rejection by the oocyte donor's immune system is typically avoided.

In a related aspect, a cell bank of hES cell lines derived from parthenogenically activated oocytes is provided.

In one embodiment, a method for producing human stem cells from a cryopreserved oocyte or parthenote is provided, including microinjecting into the cytoplasm of the oocyte or parthenote a cryopreservation agent, freezing the oocyte or parthenote to a cryogenic temperature to cause it to enter a dormant state, storing the oocyte or parthenote in the dormant state, thawing the oocyte or parthenote, parthenogenically activating the oocyte, where the activation includes contacting the oocyte with an ionophore at high O₂ tension and contacting the oocyte with a serine-threonine kinase inhibitor under low O₂ tension, cultivating the parthenote or activated oocyte under low O₂ tension until blastocyst formation, isolating an inner cell mass (ICM) from the trophectoderm of the blastocyst, and culturing the cells of the ICM on a layer of feeder cells, where culturing is carried out under high O₂ tension.

In another embodiment, autologous stem cells derived from parthenogenetically activated oocytes from a human donor are provided. In one aspect, the stem cells possess a substantially identical haplotype as the donor cell. In a related aspect, stem cells are substantially identical genetically to the donor cell.

In one aspect, a stem cell is identified as a full sibling of the donor according to single nucleotide polymorphism (SNP) markers. In another aspect, a stem cell is genomically imprinted according to donor origin.

In one embodiment, a differentiated cell derived from a stem cell obtained from a parthenogenetically activated oocyte from a human donor is disclosed. In a related aspect, the differentiated cell includes, but is not limited to, a neuronal cell, a cardiac cell, a smooth muscle cell, a striated muscle cell, an endothelial cell, an osteoblast, an oligodendrocyte, a hematopoietic cell, an adipose cell, a stromal cell, a chondrocyte, an astrocyte, a dendritic cell, a keratinocyte, a pancreatic islet, a lymphoid precursor cell, a mast cell, a mesodermal cell, and an endodermal cell. In a further related aspect, the differentiated cell expresses one or more markers, including but not limited to, neurofiliment 68, NCAM, beta III-tubulin, GFAP, alpha-actinin, desmin, PECAM-1, VE-Cadherin, alpha-fetoprotein, or a combination thereof.

In another embodiment, a cell line comprising autologous stem cells is disclosed, where the stem cells are derived from parthenogenetically activated oocytes from a human donor. In one aspect, the cells do not express S SEA-1. In another aspect, the cells of the cell line give rise to ectodermal, mesodermal, and endodermal germ lines.

In one embodiment, a cell bank is disclosed including cryopreserved parthenotes, where the parthenotes are derived from parthenogenetically activated oocytes from one or more human donors. In a related aspect, the parthenotes have been cultivated under low O₂ tension until blastocyst formation.

In one embodiment, a cell bank is disclosed including cryopreserved autologous stem cells, where the stem cells are derived from parthenogenetically activated oocytes from one or more human donors.

In another embodiment, a method of treating a subject in need thereof, comprising administering a cellular composition comprising differentiated cells, wherein the differentiated cells are derived from a stem cell obtained from a parthenogenetically activated oocyte from a human donor. In one aspect, the differentiated cell is selected from the group consisting of a neuronal cell, cardiac cell, smooth muscle cell, striated muscle cell, endothelial cell, osteoblast, oligodendrocyte, hematopoietic cell, adipose cell, stromal cell, chondrocyte, astrocyte, dendritic cell, keratinocyte, pancreatic islet, lymphoid precursor cell, mast cell, mesodermal cell, and endodermal cell.

In a related aspect, the subject presents a disease selected from the group consisting of Parkinson's disease, Huntington's disease, Alzheimer's disease, ALS, spinal cord defects or injuries, multiple sclerosis, muscular dystrophy, cystic fibrosis, liver disease, diabetes, heart disease, retinal disease (such as macular degeneration and retinitis pigmentosa), cartilage defects or injuries, burns, foot ulcers, vascular disease, urinary tract disease, AIDS, and cancer.

In one embodiment, a method of generating cloned human embryonic stem cells is disclosed, including removing a first pronuclei from a previously fertilized human oocyte, transferring a second pro-nuclei into the enucleated oocyte, where the second pro-nuclei is derived from a donor oocyte or an oocyte from the mother of the donor, or a parthenogenetically activated oocyte, where the pro-nuclei of the oocyte has been replaced by the nucleus of a donor somatic cell prior to activation, and cultivating the resulting oocyte until blastocyst formation, where an inner cell mass from the blastocyst contains the embryonic stem cells.

Exemplary methods and compositions according to this invention are described in greater detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows a micrograph of the surface marker expression of alkaline phosphatase for the parthenogenically derived hES cells.

FIG. 1B shows a micrograph of the expression for the surface marker Oct4.

FIG. 1C shows a micrograph of the expression for the surface marker SSEA-1.

FIG. 1D shows a micrograph of the expression for the surface marker SSEA-3.

FIG. 1E shows a micrograph of the expression for the surface marker SSEA-4.

FIG. 1F shows a micrograph of the expression for the surface marker TRA-1-60.

FIG. 1G shows a micrograph of the expression for the surface marker TRA-1-81.

FIG. 2A shows the analysis of telomerase activity for the parthenogenically derived hES cells. 500, 1000, and 10000 (units) of extract was used to perform the analysis. AH-heat treated test extract (negative control); positive control-telomerase positive cells; CHAPS-lysis buffer; TSR8-control template.

FIG. 2B shows a micrograph of embryoid body formation from parthenogenically derived hES cells, 9 day culture.

FIG. 2C shows a micrograph of embryoid body formation from parthenogenically derived hES cells, 10 day culture.

FIG. 2D illustrates the karyotype of parthenogenically derived hES cells.

FIG. 2E shows the results from DNA finger printing analysis of parthenogenically derived hES cells. 1—DNA from the blood of the oocyte donor; 2—DNA from the parthenogenic hES cells derived from the same donor; 3—DNA from human feeder fibroblasts.

FIG. 3 shows a Northern blot characterizing the expression of genes associated with genomic imprinting. DNA probes: SNRPN, Peg1_2, Peg1_A, H19, and GAPDH (as an internal control). NSF, neonatal skin fibroblasts; hES, human embryonic stem cell line derived from fertilized oocytes; 1, phESC-1; 2, phESC-3, 3, phESC-4, 4, phESC-5; 5, phESC-6; 6 phESC-7. NSF RT−, hES RT−, 1 RT− are negative controls.

FIG. 4 shows the differentiation of phESC into derivatives of all three germ layers. Ectoderm differentiation is presented by positive immunocytochemical staining for neuron specific markers 68 (A), NCAM (B), beta III-tubulin (C) and glial cell marker GFAP (D, M). Differentiated cells were positive for mesodermal markers: muscle specific alpha actinin (G) and desmin (J), endothelial markers PECAM-1 (E) and VE-Cadherin (F). Endoderm differentiation is presented by positive staining for alpha-fetoprotein (H, L). The phESC produce pigmented epithelial-like cells (I, K). Magnification (I) ×100; (A-H, J-M), ×400.

FIG. 5 shows the characterization of phESC lines for specific markers. Undifferentiated colonies of phESC on human feeder layer cells (A-F), negative staining for SSEA-1 (G-L), expression of cell surface markers SSEA-3 (M-R), SSEA-4 (S-X). Magnification (A) to (E) ×100; (F) ×200; (G) to (X) ×400. Alkaline phosphatase positive staining of phESC colonies on feeder cells (A-F), OCT-4 (G-L), TRA-1-60 (K-R) and TRA-1-81 (S-X). Magnification (A, B, O, R) ×100; (C-F, M, S, X) ×200; (G-L, N, P, Q, T-W) ×400.

FIG. 6 demonstrates that phESC cells possess high levels of telomerase activity by comparison with positive control cells: “+”-extract from 500 cells; “−”-heat treated cell extract with inactivated telomerase; “Control+”-telomerase positive cell extract (applied with TRAPEZE Kit); “B”-CHAPS lysis buffer, primer-dimer/PCR contamination control; TSR8-telomerase quantitative control template (0.1 and 0.2 amole/μl); “M”-marker, DNA ladder.

FIG. 7 shows the G-banded karyotyping of phESC lines. The phESC-1 (A), phESC-3 (B), phESC-4 (C), phESC-5 (D) and phESC-6 (E) lines have normal 46, XX karyotype. The phESC-7 line has 47, XXX karyotype (F).

DETAILED DESCRIPTION OF THE INVENTION

Before the present composition, methods, and culturing methodologies are described, it is to be understood that this invention is not limited to particular compositions, methods, and experimental conditions described, as such compositions, methods, and conditions may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only in the appended claims.

As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to “the method” includes one or more methods, and/or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.

“Differentiation” refers to a change that occurs in cells to cause those cells to assume certain specialized functions and to lose the ability to change into certain other specialized functional units. Cells capable of differentiation may be any of totipotent, pluripotent or multipotent cells. Differentiation may be partial or complete with respect to mature adult cells.

Gynogenesis refers to the production of an embryo containing a discernible trophectoderm and inner cell mass that results upon activation of a cell, such as an oocyte, or other embryonic cell type, containing mammalian DNA of all female origin, preferably human female origin, e.g., human or non-human primate oocyte DNA. Such female mammalian DNA may be genetically modified, e.g., by insertion, deletion or substitution of at least one DNA sequence, or may be unmodified. For example, the DNA may be modified by the insertion or deletion of desired coding sequences, or sequences that promote or inhibit embryogenesis. Typically, such an embryo will be obtained by in vitro activation of an oocyte that contains DNA of all female origin. Gynogenesis is inclusive of parthenogenesis which is defined below. It also includes activation methods where the spermatozoal DNA does not contribute to the DNA in the activated oocyte.

In a related aspect, oocytes are obtained from superovulating subjects prepared for IVF. “Superovulation” techniques, such as treatment of a female subject with hormones, used in IVF are designed to stimulate the ovaries to produce several eggs (oocytes) rather than the usual single egg as in a natural cycle.

The medications required to boost egg production may include, but are not limited to the following: Lupron (gonadotropin releasing hormone-agonist), Orgalutran, Antagon or Cetrotide (gonadotropin releasing hormone-antagonist), Follistim, Bravelle or Gonal-F (FSH, follicle stimulating hormone), Repronex (combination of FSH and LH, luteinizing hormone), and Pregnyl or Novarel (hCG, human chorionic gonadotropin).

In a related aspect, collection of eggs can be performed under transvaginal ultrasound guidance. To accomplish this, a needle is inserted (e.g., under IV sedation) through the vaginal wall into the ovaries using ultrasound to locate each follicle. The follicular fluid is drawn up into a test tube to obtain the eggs.

“Parthenogenesis” (“parthenogenically activated” and “parthenogenetically activated” is used interchangeably) the process by which activation of the oocyte occurs in the absence of sperm penetration, and refers to the development of an early stage embryo comprising trophectoderm and inner cell mass that is obtained by activation of an oocyte or embryonic cell, e.g., blastomere, comprising DNA of all female origin. In a related aspect, a “parthenote” refers to the resulting cell obtained by such activation. In another related aspect, “blastocyst” refers to a cleavage stage of a fertilized or activated oocyte comprising a hollow ball of cells made of outer trophoblast cells and an inner cell mass (ICM). In a further related aspect, “blastocyst formation” refers to the process, after oocyte fertilization or activation, where the oocyte is subsequently cultured in media for a time to enable it to develop into a hollow ball of cells made of outer trophoblast cells and ICM (e.g., 5 to 6 days).

In one embodiment, the process of creating cloned human embryonic stem cell line by parthenogenetically activated oocytes is disclosed. While pathogenesis is not an uncommon form of reproduction in nature, mammals are not known to be capable of this form of reproduction. However, a 10% rate of spontaneous parthenogenesis can be found in oocytes from females of the inbred mouse strain LT/Sv (Ozil and Huneau, Development (2001) 128:917-928; Vrana et al., Proc Natl Acad Sci USA (2003) 100(Suppl 1):11911-11916; Berkowitz and Goldstein, New Eng J Med (1996) 335(23):1740-1748). Oocytes from placental mammals can be induced to undergo parthenogenesis in vitro; however, embryonic development is unsuccessful.

Following parthenogenic activation of mammalian oocytes and transfer of the activated oocyte into a surrogate mother, there is limited embryonic survival: ten days in mice; 21 days in sheep; 29 days in pigs; and 11.5 days in rabbits (Kure-bayashi et al., Theriogenology (2000) 53:1105-1119; Hagemann et al., Mol Reprod Dev (1998) 50:154-162; Surani and Barton, Science (1983) 222:1034-1036). The reason for this arrested development is likely due to genetic imprinting. It has been shown that maternal and paternal genomes are epigentically different and that both sets are required for successful embryonic development (Surani, Cell (1998) 93:309-312; Sasaki et al., (1992) 6:1843-1856). In parthenotes, all of the genetic material should be of maternal origin, a therefore should lack paternal imprinting. Paternal imprinting is thought to be responsible for extra-embryo tissue development, thus the development of trophoblastic tissue following fertilization of an enucleated oocyte (Stevens, Nature (1978) 276:266-267). In animals, therefore, enucleated zygotes may be useful for nuclear transfer with subsequent parthenogenic activation.

Mammalian parthenotes undergo only limited development with eventual death of the embryo. In Macac fascicularis, only 14 percent of oocytes in stage II metaphase following in vitro Parthenogenetic activation developed to the blastocyst stage following 8 days of culture (Monk, Genes Dev (1988) 2:921-925). Similarly, 12 percent of human oocytes that were parthenogenetically activated in vitro following nuclear transfer developed to the blastocyst state (Monk, 1988). In both cases, one stem cell line was created.

Embryos formed in spontaneously activated parthenotes in virgin females of the LT/Sv inbred mouse strain die within a few days. When nuclear transfer is performed from cells comprising the inner cell mass (ICM) of these embryos into fertilized enucleated C57BL/6j mouse oocytes, cloned mice with the LT/Sv genome are obtained (Kaufman et al., Nature (1977) 265:53-55). Thus, the use of a fertilized oocyte allows for full-term development of a parthenote. In one aspect, a fertilized enucleated human oocyte can be used to support development of a parthenogenetic embryo containing a donor's nuclei until the blastocyst stage.

In one embodiment, the pronuclei of a donor's oocyte or from the oocyte of the mother of a donor, following parthenogenetic activation, can be transferred into a fertilized human oocyte from which the male and female pronuclei have been extracted.

In another embodiment, a two stage process is disclosed for generating human stem cells including transferring the nucleus of a donor's somatic cell into a donor oocyte, where the oocyte is subsequently activated by parthenogenesis and transferring the pronuclei of the activated oocyte into a fertilized oocyte, where the male and female pronuclei have been extracted.

In another embodiment, the nucleus from a donor's somatic cell can be transferred into a fertilized enucleated human oocyte with subsequent parthenogenetic activation. The three embodiments above are illustrated by the following flow diagrams:

“Pluripotent cell” refers to a cell derived from an embryo produced by activation of a cell containing DNA of all female or male origin that can be maintained in vitro for prolonged, theoretically indefinite period of time in an undifferentiated state, that can give rise to different differentiated tissue types, i.e., ectoderm, mesoderm, and endoderm. The pluripotent state of the cells is preferably maintained by culturing inner cell mass or cells derived from the inner cell mass of an embryo produced by androgenetic or gynogenetic methods under appropriate conditions, for example, by culturing on a fibroblast feeder layer or another feeder layer or culture that includes leukemia inhibitory factor (LIF). The pluripotent state of such cultured cells can be confirmed by various methods, e.g., (i) confirming the expression of markers characteristic of pluripotent cells; (ii) production of chimeric animals that contain cells that express the genotype of the pluripotent cells; (iii) injection of cells into animals, e.g., SCID mice, with the production of different differentiated cell types in vivo; and (iv) observation of the differentiation of the cells (e.g., when cultured in the absence of feeder layer or LIF) into embryoid bodies and other differentiated cell types in vitro.

“Diploid cell” refers to a cell, e.g., an oocyte or blastomere, having a diploid DNA content of all male or female origin.

“Haploid cell” refers to a cell, e.g., an oocyte or blastomere, having a haploid DNA content, where the haploid DNA is of all male or female origin.

Activation refers to a process where a fertilized or unfertilized oocyte, for example, but not limited to, in metaphase II of meiosis, undergoes a process typically including separation of the chromatid pairs, extrusion of the second polar body, resulting in an oocyte having a haploid number of chromosomes, each with one chromatid. Activation includes methods whereby a cell containing DNA of all male or female origin is induced to develop into an embryo that has a discernible inner cell mass and trophectoderm, which is useful for producing pluripotent cells but which is itself is likely to be incapable of developing into a viable offspring. Activation may be carried out, for example, under one of the following conditions: (1) conditions that do not cause second polar body extrusion; (ii) conditions that cause polar body extrusion but where the polar body extrusion is inhibited; or (iii) conditions that inhibit first cell division of the haploid oocyte.

“Metaphase II” refers to a stage of cell development where the DNA content of a cell consists of a haploid number of chromosomes with each chromosome represented by two chromatids.

In one embodiment, metaphase II oocytes are activated by incubating oocytes under various O₂ tension gas environments. In a related aspect, the low O₂ tension gas environment is created by a gas mixture comprising an O₂ concentration of about 2%, 3%, 4%, or 5%. In a further related aspect, the gas mixture comprises about 5% CO₂. Further, the gas mixture comprises about 90% N₂, 91% N₂, or 93% N₂. This gas mixture is to be distinguished from 5% CO₂ air, which is approximately about 5% CO₂, 20% 02, and 75% N₂.

“O₂ tension” refers to the partial pressure (pressure exerted by a single component of a gas mixture) of oxygen in a fluid (i.e., liquid or gas). Low tension is when the partial pressure of oxygen (pO₂) is low and high tension is when the pO₂ is high.

“Defined-medium conditions” refer to environments for culturing cells where the concentration of components therein required for optimal growth are detailed. For example, depending on the use of the cells (e.g., therapeutic applications), removing cells from conditions that contain xenogenic proteins is important; i.e., the culture conditions are animal-free conditions or free of non-human animal proteins. In a related aspect, “in vitro fertilization (IVF) media” refers to a nutrient system which contains chemically defined substances on or in which fertilized oocytes can be grown.

“Extracellular matrix (ECM) substrates” refer to a surface beneath cells which supports optimum growth. For example, such ECM substrates include, but are not limited to, Matrigel, laminin, gelatin, and fibronectin substrates. In a related aspect, such substrates may comprise collagen IV, entactin, heparin sulfate proteoglycan, to include various growth factors (e.g., bFGF, epidermal growth factor, insulin-like growth factor-1, platelet derived growth factor, nerve growth factor, and TGF-β-1).

“Embryo” refers to an embryo that results upon activation of a cell, e.g., oocyte or other embryonic cells containing DNA of all male or female origin, which optionally may be modified, that comprises a discernible trophectoderm and inner cell mass, which cannot give rise to a viable offspring and where the DNA is of all male or female origin. The inner cell mass or cells contained therein are useful for the production of pluripotent cells as defined previously.

“Inner cell mass (ICM)” refers to the inner portion of an embryo which gives rise to fetal tissues. Herein, these cells are used to provide a continuous source of pluripotent cells in vitro. Further, the ICM includes the inner portion of the embryo that results from androgenesis or gynogenesis, i.e., embryos that result upon activation of cells containing DNA of all male or female origin. Such DNA, for example, will be human DNA, e.g., human oocyte or spermatozoal DNA, which may or may not have been genetically modified.

“Trophectoderm” refers to another portion of early stage embryo which gives rise to placental tissues, including that tissue of an embryo that results from androgenesis or gynogenesis, i.e., embryos that result from activation of cells that contain DNA of all male or female origin, e.g., human ovarian or spermatozoan.

“Differentiated cell” refers to a non-embryonic cell that possesses a particular differentiated, i.e., non-embryonic, state. The three earliest differentiated cell types are endoderm, mesoderm, and ectoderm.

“Substantially identical” refers to a quality of sameness regarding a particular characteristic that is so close as to be essentially the same within the ability to measure difference (e.g., by HLA typing, SNP analysis, and the like).

“Histocompatible” refers to the extent to which an organism will tolerate a graft of a foreign tissue.

“Genomic imprinting” refers to the mechanism by which a number of genes throughout the genome are monoallelically expressed according to their parental origin.

“Homoplasmy,” including grammatical variations thereof, refers to the presence of the same type of the mitochondrial DNA (mtDNA) within a cell or individual.

“Heteroplasmy,” including grammatical variations thereof, refers to the presence of a mixture of more than one type of mitochondrial DNA (mtDNA) within a cell or individual.

“Uniparental” refers to one or more cells or individuals from which another arises and to which it remains subsidiary.

“Mechanically isolating” refers to the process of separating cell aggregates by physical forces. For example, such a process would exclude the use of enzymes (or other cell cleavage products) which might contain non-human materials.

In the native environment, immature oocytes (eggs) from the ovary undergo a process of maturation which results in the progression through meiosis to metaphase II of meiosis. The oocytes then arrest at metaphase II. In metaphase II, the DNA content of the cell consists of a haploid number of chromosomes, each represented by two chromatids.

Such oocytes may be maintained indefinitely by cryopreserving by, for example, but not limited to, microinjection with a sugar.

In one embodiment, a method for producing human stem cells from a cryopreserved oocyte or parthenote is provided, including microinjecting into the cytoplasm of the oocyte or parthenote a cryopreservation agent, freezing the oocyte or parthenote to a cryogenic temperature to cause it to enter a dormant state, storing the oocyte or parthenote in the dormant state, thawing the oocyte or parthenote, parthenogenically activating the oocyte under high O₂ tension in the presence or an ionophore followed by contacting the oocyte with a serine-threonine kinase inhibitor under low O₂ tension, culturing the activated oocyte or parthenote until blastocyst formation, isolating an inner cell mass (ICM) from the blastocyst, and culturing the cells of the ICM on a layer of human feeder cells, where culturing the ICM cells is carried out under high O₂ tension.

In one aspect, oocytes obtained as described are transferred to modified, isotonic IVF covered with embryo-tested mineral oil (Sigma), or any other suitable medium. If desired, the oocytes may be incubated with an extracellular sugar at the same concentration as the amount planned for microinjection. For example, to inject 0.1 M sugar, oocytes may be equilibrated in DMEM/F-12 with 0.1 M sugar. In one aspect, the cryopreservation agent comprises a lower Na⁺ concentration than standard DMEM (i.e., Na⁺ low media). In a related aspect, the cryopreservation agent comprises a higher K⁺ concentration than standard DMEM (i.e., K⁺ high). In a further related aspect, the cryopreservation agent comprises both a lower Na⁺ and higher K⁺ concentration than standard DMEM (i.e., Na⁺ low/K⁺ high media). In one aspect, the cryopreservation agent comprises an organic buffer, including but not limited to, HEPES. In another aspect, the cryopreservation agent comprises moieties that inhibit apoptotic protein (e.g., capases).

Alternatively, the oocytes may be optionally equilibrated with any other substantially non-permeable solute, such a NaCl, to decrease their cell volume prior to microinjection. This initial decrease in cell volume may result in a smaller final volume of the microinjected oocytes compared to oocytes not incubated in a hypertonic media prior to microinjection. This smaller final volume may minimize any potential adverse effect from the swelling of the oocytes. This general procedure for the preparation of cells for microinjection may also be used for other cell types (e.g., activated oocytes, hES cells, and the like).

The oocytes are then microinjected with a cryopreservation agent. Microinjection equipment and procedures are well characterized in the art and microinjection equipment known for use in injecting small molecules into cells may be used with the invention. In an exemplary microinjection step, oocytes can be microinjected at a pressure of 10 psi for 30 milliseconds. Another example of a standard microinjection technique is the method described by Nakayama and Yanagimachi (Nature Biotech. 16:639-642, 1998).

A cryopreservation agent useful in this process includes any chemical that has cryo-protective properties and is ordinarily non-permeable. In particular, the cryopreservation agent can include sugars either alone or mixed together with other traditional cryopreservation agents. Carbohydrate sugars such as trehalose, sucrose, fructose, and raffinose, may be microinjected to concentrations less than or equal to about 1.0 M, and more preferably, less than or equal to about 0.4 M. In one aspect, the concentration is between 0.05 and 0.20 M, inclusive. Additionally, an extracellular sugar or traditional cryopreservation agent may be added prior to storage. If the cells were incubated in a hypertonic solution prior to microinjection, the substantially non-permeable solute may be allowed to remain in the media after microinjection or may be removed from the media by washing the cells with media containing a lower concentration, or none, of this solute.

Certain sugars or polysaccharides which ordinarily do not permeate cell membranes because they are too large to pass through the membrane have superior physiochemical and biological properties for cryopreservation purposes. While these sugars ordinarily do not permeate cell membranes on their own, using the method as described, these ordinarily non-permeating sugars may be microinjected intracellularly to result in a beneficial effect.

Non-permeating sugars having a stabilizing or preserving effect on cells that are especially useful as the cryopreservation agent in the present method include sucrose, trehalose, fructose, dextran, and raffinose. Among these sugars, trehalose, a non-reducing disaccharide of glucose, has been shown to be exceptionally effective in stabilizing cell structures at low concentrations. The addition of extracellular glycolipids or glycoproteins may also stabilize the cell membrane.

Following the microinjection of the cryopreservation agent, the cells are prepared for storage. A variety of methods for freezing and/or drying may be employed to prepare the cells for storage. In particular, three approaches are described herein: vacuum or air drying, freeze drying, and freeze-thaw protocols. Drying processes have the advantage that the stabilized biological material may be transported and stored at ambient temperatures.

Typically, oocytes loaded with 1 to 2M DMSO are cooled at a very slow cooling rate (0.3 to 0.5° C./min) to an intermediate temperature (−60° C. to −80° C.) before plunging in liquid nitrogen for storage. The sample can then be stored at this temperature.

The suspended material can then be stored at cryopreservation temperatures, for example, by leaving the vials in liquid nitrogen (LN₂), for the desired amount of time.

Protocols for vacuum or air drying and for freeze drying proteins are well characterized in the art (Franks et al., “Materials Science and the Production of Shelf-Stable Biologicals,” BioPharm, October 1991, p. 39; Shalaev et al., “Changes in the Physical State of Model Mixtures during Freezing and Drying: Impact on Product Quality,” Cryobiol. 33, 14-26 (1996)) and such protocols may be used to prepare cell suspensions for storage with the method as described. In addition to air drying, other convective drying methods that may be used to remove water from cell suspensions include the convective flow of nitrogen or other gases.

An exemplary evaporative vacuum drying protocol useful with the method of the invention may include placing 20 μl each into wells on 12 well plates and vacuum drying for 2 hours at ambient temperature. Of course, other drying methods could be used, including drying the cells in vials. Cells prepared in this manner may be stored dry, and rehydrated by diluting in DMEM or any other suitable media.

A method of the invention using freeze drying to prepare the cells for storage begins with freezing the cell suspension. While methods of freezing known in the art may be employed, the simple plunge freezing method described herein for the freeze-thaw method may also be used for the freezing step in the freeze drying protocol.

After freezing, a two stage drying process may be employed. In the first stage, energy of sublimation is added to vaporize frozen water. Secondary drying is performed after the pure crystalline ice in the sample has been sublimated. Freeze dried cells can be stored and hydrated in the same manner as described above for vacuum drying. Viable cells may then be recovered.

After the recovery of cells from a frozen or dried state, any external cryopreservation agent may be optionally removed from the culture media. For example, the media may be diluted by the addition of the corresponding media with a lower concentration of cryopreservation agent. For example, the recovered cells may be incubated for approximately five minutes in media containing a lower concentration of sugar than that used for cell storage. For this incubation, the media may contain the same sugar that was used as the cryopreservation agent; a different cryopreservation agent, such as galactose; or any other substantially non-permeable solute. To minimize any osmotic shock induced by the decrease in the osmolarity of the media, the concentration of the extracellular cryopreservation agent may be slowly decreased by performing this dilution step multiple times, each time with a lower concentration of cryopreservation agent. These dilution steps may be repeated until there is no extracellular cryopreservation agent present or until the concentration of cryopreservation agent or the osmolarity of the media is reduced to a desired level.

The parthenogenetically activated oocytes, blastocysts, ICM, and autologous stem cells can be stored or “banked” in a manner that allows the cells to be revived as needed in the future. An aliquot of the parthenogenetically activated oocytes and autologous stem cells can be removed at any time, to be grown into cultures of many undifferentiated cells and then differentiated into a particular cell type or tissue type, and may then be used to treat a disease or to replace malfunctioning tissues in a subject. Since the cells are parthenogenetically derived from the donor, the cells can be stored so that an individual or close relative can have access to cells for an extended period of time.

In one embodiment, a cell bank is provided for storing parthenogenetically activated oocytes, blastocysts, ICM, and/or autologous stem cell samples. In another embodiment, methods for administering such a cell bank are provided. U.S. Published Patent Application No. 20030215942, which is incorporated by reference herein in its entirety, provides an example of a stem cell bank system.

Using methods such as those described above, the isolation and in vitro propagation of parthenogenetically activated oocytes, blastocysts, ICM, and autologous stem cell samples and their cryopreservation facilitates the establishment of a “bank” of transplantable human stem cells. Because it is possible to store smaller aliquots of cells, the banking procedure could take up a relatively small space. Therefore, the cells of many individuals could be stored or “banked” on a short term or long term basis, with relatively little expense.

In one embodiment, a portion of the sample is made available for testing, either before or after processing and storage.

This invention also provides methods of recording or indexing the parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell samples so that when a sample needs to be located, it can be easily retrieved. Any indexing and retrieval system can be used to fulfill this purpose. Any suitable type of storage system can be used so that the parthenogenetically activated oocytes, blastocysts, ICM, and/or autologous stem cells can be stored. The samples can be designed to store individual samples, or can be designed to store hundreds, thousands, and even millions of different cell samples.

The stored parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell samples can be indexed for reliable and accurate retrieval. For example, each sample can be marked with alphanumeric codes, bar codes, or any other method or combinations thereof. There may also be an accessible and readable listing of information enabling identification of each parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell sample and its location in the bank and enabling identification of the source and/or type the cell sample, which is outside of the bank. This indexing system can be managed in any way known in the art, e.g., manually or non-manually, e.g., a computer and conventional software can be used.

In one embodiment, the cell samples are organized using an indexing system so that the sample will be available for the donor's use whenever needed. In other embodiments, the cell samples can be utilized by individuals related to the original donor. Once recorded into the indexing system, the cell sample can be made available for matching purposes, e.g., a matching program will identify an individual with matching type information and the individual will have the option of being provided the matching sample.

The storage banking system can comprise a system for storing a plurality of records associated with a plurality of individuals and a plurality of cell samples. Each record may contain type information, genotypic information or phenotypic information associated with the cell samples or specific individuals. In one embodiment, the system will include a cross-match table that matches types of the samples with types of individuals who wish to receive a sample.

In one embodiment, the database system stores information for each parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell sample in the bank. Certain information is stored in association with each sample. The information may be associated with a particular donor, for example, an identification of the donor and the donor's medical history. For example, each sample may be HLA typed and the HLA type information may be stored in association with each sample. The information stored may also be availability information. The information stored with each sample is searchable and identifies the sample in such a way that it can be located and supplied to the client immediately.

Accordingly, embodiments of the invention utilize computer-based systems that contain information such as the donor, date of submission, type of cells submitted, types of cell surface markers present, genetic information relating to the donor, or other pertinent information, and storage details such as maintenance records and the location of the stored samples, and other useful information.

The term “a computer-based system” refers to the hardware, software, and any database used to store, search, and retrieve information about the stored cells. The computer-based system preferably includes the storage media described above, and a processor for accessing and manipulating the data. The hardware of the computer-based systems of this embodiment comprises a central processing unit (CPU) and a database. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable.

In one embodiment, the computer system includes a processor connected to a bus that is connected to a main memory (preferably implemented as RAM) and a variety of secondary storage devices, such as a hard drive and removable medium storage device. The removable medium storage device can represent, for example, a floppy disk drive, a DVD drive, an optical disk drive, a compact disk drive, a magnetic tape drive, etc. A removable storage medium, such as a floppy disk, a compact disk, a magnetic tape, etc. containing control logic and/or data recorded therein can be inserted into the removable storage device. The computer system includes appropriate software for reading the control logic and/or the data from the removable medium storage device once inserted in the removable medium storage device. Information relating to the parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell can be stored in a well-known manner in the main memory, any of the secondary storage devices, and/or a removable storage medium. Software for accessing and processing these data (such as search tools, compare tools, etc.) reside in main memory during execution.

As used herein, “a database” refers to memory that can store any useful information relating to the parthenogenetically activated oocyte and/or autologous stem cell collections and the donors.

The data relating to the stored parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell can be stored and manipulated in a variety of data processor programs in a variety of formats. For example, the data can be stored as text in a word processing file, such as Microsoft WORD or WORDPERFECT, an ASCII file, an html file, or a pdf file in a variety of database programs familiar to those of skill in the art, such as DB2, SYBASE, or ORACLE.

A “search program” refers to one or more programs that are implemented on the computer-based system to search for details or compare information relating to the cryopreserved samples within a database. A “retrieval program” refers to one or more programs that can be implemented on the computer-based system to identify parameters of interest in the database. For example, a retrieval program can be used to find samples that fit a particular profile, samples having specific markers or DNA sequences, or to find the location of samples corresponding to particular individuals.

There is no upper limit on the number of cell samples that can be stored in one cell bank. In one embodiment, hundreds of products from different individuals will be stored at one bank or storage facility. In another embodiment, up to millions of products may be stored in one storage facility. A single storage facility may be used to store parthenogenetically activated oocyte and/or autologous stem cell samples, or multiple storage facilities may be used.

In some embodiments of the present invention, the storage facility may have a means for any method of organizing and indexing the stored cell samples, such as, for example, automated robotic retrieval mechanisms and cell sample manipulation mechanisms. The facility may include micromanipulation devices for processing cell samples. Known conventional technologies can be used for efficient storage and retrieval of the cell samples. Exemplary technologies include but are not limited to Machine Vision, Robotics, Automated Guided Vehicle System, Automated Storage and Retrieval Systems, Computer Integrated Manufacturing, Computer Aided Process Planning, Statistical Process Control, and the like.

The type information or other information associated with the individual in need of a sample may be recorded into a system that can be used to identify an appropriate matching product, such as, for example, a database system, an indexing system, and the like. Once recorded in the system, a match can be made between the type of the individual and a donor cell sample. In preferred embodiments, the donor sample is from the same individual as the individual in need of the sample. However, similar but not identical donor/recipient matches can also be used. The matching sample is available for the individual possessing the matching type identifier. In one embodiment of this invention, the individual's identification information is stored in connection with the cell sample. In some embodiments, the matching process occurs around the time of harvesting the sample, or can occur at any time during processing, storage, or when a need arises. Accordingly, in some embodiments of the invention, the matching process occurs before the individual is in actual need of the cell sample.

When the parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell sample is needed by an individual, it may be retrieved and made available for research, transplantation or other purposes within minutes, if desired. The sample may also be further processed to prepare it for transplantation or other needs.

Normally, the oocyte is ovulated at this stage and fertilized by the sperm. The sperm initiates the completion of meiosis in a process called activation. During activation, the pairs of chromatids separate, the second polar body is extruded, and the oocyte retains a haploid number of chromosomes, each with one chromatid. The sperm contributes the other haploid complement of chromosomes to make a full diploid cell with single chromatids. The chromosomes then progress through DNA synthesis during the first cell cycle. These cells then develop into embryos.

By contrast, embryos described herein are developed by artificial activation of cells, typically mammalian oocytes or blastomeres containing DNA of all male or female origin. As discussed in the background of the invention, many methods have been reported in the literature for artificial activation of unfertilized oocytes. Such methods include physical methods, e.g., mechanical methods such as pricking, manipulation or oocytes in culture, thermal methods such as cooling and heating, repeated electric pulses, enzymatic treatments, such as trypsin, pronase, hyaluronidase, osmotic treatments, ionic treatments such as with divalent cations and calcium ionophores, such as ionomycin and A23187, the use of anesthetics such as ether, ethanol, tetracaine, lignocaine, procaine, phenothiazine, tranquilizers such as thioridazine, trifluoperazine, fluphenazine, chlorpromazine, the use of protein synthesis inhibitors such as cycloheximide, puromycin, the use of phosphorylation inhibitors, e.g., protein kinase inhibitors such as staurosporine, 2-aminopurine, sphingosine, and DMAP, combinations thereof, as well as other methods.

Such activation methods are well known in the art and are discussed U.S. Pat. No. 5,945,577, incorporated herein by reference.

In one embodiment, a human cell in metaphase II, typically an oocyte or blastomere comprising DNA of all male or female origin, is artificially activated for effecting artificial activation of oocytes.

In a related aspect, the activated cell, e.g., oocyte, which is diploid, is allowed to develop into an embryo that comprises a trophectoderm and an inner cell mass. This can be effected using known methods and culture media that facilitate blastocyst development.

After the gynogenetic embryos have been cultured to produce a discernable trophectoderm and inner cell mass, the cells of the inner cell mass are then used to produce the desired pluripotent cell lines. This can be accomplished by transferring cells derived from the inner cell mass or the entire inner cell mass onto a culture that inhibits differentiation. This can be effected by transferring the inner cell mass cells onto a feeder layer that inhibits differentiation, e.g., fibroblasts or epithelial cells, such as fibroblasts derived from postnatal human tissues, etc., or other cells that produce LIF. Other factors/components may be employed to provide appropriate culture conditions for maintaining cells in the undifferentiated state including, but not limited to, addition of conditioned media (Amit et al., Developmental Biol (2000) 227:271-278), bFGF and TGF-β1 (with or without LIF) (Amit et al., Biol Reprod (2004) 70:837-845), factors which activate the gp130/STAT3 pathway (Hoffman and Carpenter, Nature Biotech (2005) 23(6):699-708), factors which activate the PI3K/Akt, PKB pathway (Kim et al., FEBS Lett (2005) 579:534-540), factors that are members of the bone morphogenetic protein (BMP) super family (Hoffman and Carpenter (2005), supra), and factors which activate the canonical/β-catenin Wnt signaling pathway (e.g., GSK-3-specific inhibitor; Sato et al., Nat Med (2004) 10:55-63). In a related aspect, such factors may comprise culture conditions that include feeder cells and/or ECM substrates (Hoffman and Carpenter (2005), supra).

In one aspect, the inner cell mass cells are cultured on human postnatal foreskin or dermal fibroblast cells or other cells which produce leukemia inhibitory factor, or in the presence of leukemia inhibitory factor. In a related aspect, feeder cells are inactivated prior to seeding with the ICM. For example, the feeder cells can be mitotically inactivated using an antibiotic. In a related aspect, the antibiotic can be, but is not limited to, mitomycin C.

Culturing will be effected under conditions that maintain the cells in an undifferentiated, pluripotent state, for prolonged periods, theoretically indefinitely. In one embodiment, oocytes are parthenogenically activated with calcium ionophores under high O₂ tension followed by contacting the oocytes with a serine-threonine kinase inhibitor under low O₂ tension. The resulting ICM from the parthenogenically activated oocytes is cultured under high O₂ tension, where the cells, for example, are maintained using a gas mixture comprising 20% 02. In one aspect, culturable refers to being capable of, or fit for, being cultivated. In a related aspect, ICM isolation is carried out mechanically after four days of blastocyst cultivation, where the cultivation is carried out on feeder cells. Such cultivation, for example, eliminates the need to use materials derived from animal sources, as would be the case for immunosurgery.

In a related aspect, culture media for the ICM is supplemented with non-animal sera, including but not limited to, human umbilical cord serum, where the serum is present in defined media (e.g., IVF, available from MediCult A/S, Denmark; Vitrolife, Sweden; or Zander IVF, Inc., Vero Beach, Fla.). In another aspect, the media and processes as provided are free of animal products. In a related aspect, animal products are those products, including serum, interferons, chemokines, cytokines, hormones, and growth factors, that are from non-human sources.

The pluripotent state of the cells produced by the present invention can be confirmed by various methods. For example, the cells can be tested for the presence or absence of characteristic ES cell markers. In the case of human ES cells, examples of such markers are identified supra, and include SSEA-4, SSEA-3, TRA-1-60, TRA-1-81 and OCT 4, and are known in the art.

Also, pluripotency can be confirmed by injecting the cells into a suitable animal, e.g., a SCID mouse, and observing the production of differentiated cells and tissues. Still another method of confirming pluripotency is using the subject pluripotent cells to generate chimeric animals and observing the contribution of the introduced cells to different cell types. Methods for producing chimeric animals are well known in the art and are described in U.S. Pat. No. 6,642,433, incorporated by reference herein.

Yet another method of confirming pluripotency is to observe ES cell differentiation into embryoid bodies and other differentiated cell types when cultured under conditions that favor differentiation (e.g., removal of fibroblast feeder layers). This method has been utilized and it has been confirmed that the subject pluripotent cells give rise to embryoid bodies and different differentiated cell types in tissue culture.

The resultant pluripotent cells and cell lines, preferably human pluripotent cells and cell lines, which are derived from DNA of entirely female original, have numerous therapeutic and diagnostic applications. Such pluripotent cells may be used for cell transplantation therapies or gene therapy (if genetically modified) in the treatment of numerous disease conditions.

In this regard, it is known that mouse embryonic stem (ES) cells are capable of differentiating into almost any cell type. Therefore, human pluripotent (ES) cells produced according to the invention should possess similar differentiation capacity. The pluripotent cells according to the invention will be induced to differentiate to obtain the desired cell types according to known methods. For example, human ES cells produced according to the invention may be induced to differentiate into hematopoietic stem cells, muscle cells, cardiac muscle cells, liver cells, islet cells, retinal cells, cartilage cells, epithelial cells, urinary tract cells, etc., by culturing such cells in differentiation medium and under conditions which provide for cell differentiation. Medium and methods which result in the differentiation of ES cells are known in the art as are suitable culturing conditions.

For example, Palacios et al, Proc. Natl. Acad. Sci., USA, 92:7530-7537 (1995) teach the production of hematopoietic stem cells from an embryonic cell line by subjecting stem cells to an induction procedure comprising initially culturing aggregates of such cells in a suspension culture medium lacking retinoic acid followed by culturing in the same medium containing retinoic acid, followed by transferal of cell aggregates to a substrate which provides for cell attachment.

Moreover, Pedersen, J. Reprod. Fertil. Dev., 6:543-552 (1994) is a review article which references numerous articles disclosing methods for in vitro differentiation of embryonic stem cells to produce various differentiated cell types including hematopoietic cells, muscle, cardiac muscle, nerve cells, among others.

Further, Bain et al, Dev. Biol., 168:342-357 (1995) teach in vitro differentiation of embryonic stem cells to produce neural cells which possess neuronal properties. These references are exemplary of reported methods for obtaining differentiated cells from embryonic or stem cells. These references and in particular the disclosures therein relating to methods for differentiating embryonic stem cells are incorporated by reference in their entirety herein. Thus, using known methods and culture medium, one skilled in the art may culture the subject ES cells, including genetically engineered or transgenic ES cells, to obtain desired differentiated cell types, e.g., neural cells, muscle cells, hematopoietic cells, etc. Pluripotent cells produced by the methods described herein may be used to obtain any desired differentiated cell type. Therapeutic usages of differentiated human cells are unparalleled. For example, human hematopoietic stem cells may be used in medical treatments requiring bone marrow transplantation. Such procedures are used to treat many diseases, e.g., late stage cancers such as ovarian cancer and leukemia, as well as diseases that compromise the immune system, such as AIDS. Hematopoietic stem cells can be obtained, e.g., by incorporating male or female DNA derived from a male or female cancer or AIDS patient with an enucleated oocyte, obtaining pluripotent cells as described above, and culturing such cells under conditions which favor differentiation, until hematopoietic stem cells are obtained. Such hematopoietic cells may be used in the treatment of diseases including cancer and AIDS.

Alternatively, the subject pluripotent cells may be used to treat a patient with a neurological disorder by culturing such cells under differentiation conditions that produce neural cell lines. Specific diseases treatable by transplantation of such human neural cells include, by way of example, Parkinson's disease, Alzheimer's disease, ALS and cerebral palsy, among others. In the specific case of Parkinson's disease, it has been demonstrated that transplanted fetal brain neural cells make the proper connections with surrounding cells and produce dopamine. This can result in long-term reversal of Parkinson's disease symptoms. In a related aspect, nerve precursors can be used to reanneal severed/damaged nerve fibers to restore movement after hand, leg, and spinal cord injuries.

One object of the subject invention is that it provides an essentially limitless supply of pluripotent, human cells that can be used to produce differentiated cells suitable for autologous transplantation for the oocyte donor. Human embryonic stem cells and their differentiated progeny derived from blastocysts remaining after infertility treatments, or created using NT, will likely be rejected by a recipient's immune system when used in allogenic cell transplantation therapy. Parthenogenically derived stem cells should result in differentiated cells that could alleviate the significant problem associated with current transplantation methods, i.e., rejection of the transplanted tissue which may occur because of host-vs-graft or graft-vs-host rejection relative to the oocyte donor. Conventionally, rejection is prevented or reduced by the administration of anti-rejection drugs such as cyclosporin. However, such drugs have significant adverse side-effects, e.g., immunosuppression, carcinogenic properties, as well as being very expensive. Cells produced by the methods as disclosed should eliminate, or at least greatly reduce, the need for anti-rejection drugs relative to the oocyte donor.

Another object of the subject invention is that it provides an essentially limitless supply of pluripotent, human cells that can be used to produce differentiated cells suitable for allogenic transplantation to members of the oocyte donor's family (e.g., siblings). The cells will be immunologically and genetically similar to those of the oocytes donor's direct family members and thus less likely to be rejected by the donor's family members.

Another object of this method is that parthenogenic activation of mammalian oocytes is a relatively simple procedure when compared to SCNT and results in the creation of stem cells with less cell manipulation.

Parthenogenic activation of mammalian oocytes has shown to be more efficient in the creation of stem cells than methods requiring mechanical manipulation of the oocyte (e.g., SCNT).

One drawback of SCNT is that subjects with deficient mitochondrial respiratory chain activity present phenotypes with striking similarities to abnormalities commonly encountered in SCNT fetuses and offspring (Hiendleder et al, Repro Fertil Dev (2005) 17(1-2):69-83). Cells normally contain only one type of mitochondrial DNA (mtDNA), termed homoplasmy, however, heteroplasmy does exist, usually as a combination of mutant and wild-type mt DNA molecules or form a combination of wild-type variants (Spikings et al., Hum Repro Update (2006) 12(4):401-415). As heteroplasmy can result in mitochondrial disease, various mechanisms exist to ensure maternal-only transmission. However, with the increasing use of protocols which bypass normal mechanisms for homoplasmy maintenance (e.g., cytoplasmic transfer (CT) and SCNT), perturbed mitochondrial function may be intrinsic to stem cells derived from these sources.

In one aspect, as the parthenotes are uniparental, the possibility of heteroplasmy is minimized.

Other diseases and conditions treatable by cell therapy include, by way of example, spinal cord injuries, multiple sclerosis, muscular dystrophy, diabetes, liver diseases Including acute diseases (viral hepatitis, drug overdoses (acetaminophen) and others), chronic diseases (chronic hepatitis and others (generally leading to cirrhosis)), heritable liver defects (hemophilia B, factor IX deficiency, bulirubin metabolism defects, urea cycle defects, lysosomal storage disease, al-antitrypsin deficiency and others), heart diseases, cartilage replacement, burns, foot ulcers, gastrointestinal diseases, vascular diseases, kidney disease, retinal disease, urinary tract disease, and aging related diseases and conditions.

This methodology can be used to replace defective genes, e.g., defective immune system genes, cystic fibrosis genes, or to introduce genes which result in the expression of therapeutically beneficial proteins such as growth factors, lymphokines, cytokines, enzymes, etc.

For example, the gene encoding brain derived growth factor may be introduced into human pluripotent cells produced according to the invention, the cells differentiated into neural cells and the cells transplanted into a Parkinson's patient to retard the loss of neural cells during such disease.

Also, the subject pluripotent human ES cells, may be used as an in vitro model of differentiation, in particular for the study of genes which are involved in the regulation of early development. Also, differentiated cell tissues and organs produced using the subject ES cells may be used in drug studies.

Further, the subject ES cells or differentiated cells derived therefrom may be used as nuclear donors for the production of other ES cells and cell colonies.

Still further, pluripotent cells obtained according to the present disclosure may be used to identify proteins and genes that are involved in embryogenesis. This can be effected, e.g., by differential expression, i.e., by comparing mRNAs that are expressed in pluripotent cells provided according to the invention to mRNAs that are expressed as these cells differentiate into different cell types, e.g., neural cells, myocardiocytes, other muscle cells, skin cells, etc. Thereby, it may be possible to determine what genes are involved in differentiation of specific cell types.

Further, ES cells and/or their differentiated progeny that have specific genetic defects, such as the genetic defect that leads to Duchene's Muscular Dystrophy, may be used as models to study the specific disease associated with the genetic defect.

Also, it is another object of the present disclosure to expose pluripotent cell lines produced according to the described methods to cocktails of different growth factors, at different concentrations and under different cell culture conditions such as cultured on different cell matrices or under different partial pressures of gases so as to identify conditions that induce the production and proliferation of desired differentiated cell types.

The following examples are intended to illustrate but not limit the invention.

Example 1 Production of Human Parthenogenic Embryogenic Stem Cells Materials and Methods

Donors voluntarily donated oocytes, cumulous cells, and blood (for DNA analysis) with no financial payment. Donors signed comprehensive informed consent documents and were informed that all donated materials were to be used for research and not for reproductive purposes. Before ovarian stimulation, oocyte donors underwent medical examination for suitability according to FDA eligibility determination guidelines for donors of human cells, tissues, and cellular and tissue-based products (Food and Drug Administration. (Draft) Guidance for Industry: Eligibility Determination for Donors of Human Cells, Tissues, and Cellular and Tissue Based Products (HCT/Ps) dated May 2004) and order N 67 (02.26.03) of Russian Public Health Ministry. It included X-ray, blood and urine analysis, and liver function test. Donors were also screened for syphilis, HIV, HBV, and HCV.

Oocytes were obtained using standard hormonal stimulation to produce superovulation in the subject donor. Each donor egg underwent ovarian stimulation by FSH from the 3rd to the 13th days of their menstrual cycle. A total of 1500 IU of FSh was given. From the 10th to the 14th day of the donor's menstrual cycle, gonadoliberin antagonist Orgalutran (Organon, Holland) was injected at 0.25 mg/day. From the 12th to the 14th day of the donor's menstrual cycle a daily injection of 75 IU FSH+75 IU LH (Menopur, Ferring GmbH, Germany) was given. If an ultrasound examination displayed follicles between 18 and 20 mm in diameter, a single 8000 IU dose of hGC (Choragon, Ferring GmbH, Germany) was administered on the 14th day of the donor's menstrual cycle. Trans-vaginal punction was performed 35 hours after hCG injection on approximately the 16th day. Follicular fluid was collected from the antral follicles of anesthetized donors by ultrasound-guided needle aspiration into sterile tubes.

Cumulus oocyte complexes (COCs) were picked from the follicular fluid, washed in Flushing Medium (MediCult) and then incubated in Universal IVF medium (MediCult, see Table 1) with a Liquid Paraffin (MediCult) overlay for 2 hours in a 20% 02, 5% CO₂, at 37° C. humidified atmosphere.

TABLE 1 IVF Media COMPOSITION Calcium Chloride EDTA Glucose Human Serum Albumin Magnesium Sulfate Penicillin G Potassium Chloride Potassium di-Hydrogen Phosphate Sodium Bicarbonate Sodium Chloride Sodium Lactate Sodium Pyruvate Water

Before activation, cumulus-oocyte complexes (COCs) were treated with SynVitro Hyadase (MediCult, A/S, Denmark) to remove cumulus cells followed by incubation in Universal IVF medium with a paraffin overlay for 30 minutes.

From this point onward, the culture of oocytes and embryos was performed in a humidified atmosphere at 37° C. using 02-reduced gas mixture (90% N₂₊₅% O₂+5% CO₂), with the exception of the ionomycin treatment. The oocytes were activated by incubation in 5 μM ionomycin for 5 minutes in a CO₂ incubator at 37° C. in a gas environment of 20% O₂, 5% CO₂, followed by culture with 1 mM 6-dimethylaminopurine (DMAP) for 4 hours in IVF medium, with paraffin overlay, in a gas environment of 90% N₂, 5% 02, and 5% CO₂ at 37° C. The oocytes were then washed 3 times in IVF. Activation and cultivation were carried out in 4-well plates (Nunclon, A/S, Denmark) in 500 μl of medium overlaid with liquid paraffin oil (MediCult, A/S, Denmark).

Activated oocytes were cultivated in IVF medium in a gas environment comprising 5% 02, 5% CO₂, and 90% N₂, and embryos generated from the activated oocytes were cultured in the same gas mixture.

Activated oocytes were allowed to incubate in IVF under the above conditions (i.e., low O₂ tension) until fully expanded blastocysts containing an inner cell mass (ICM) at a Blastocyst Scoring Modification of 1AA or 2AA (Shady Grove Fertility Center, Rockville, Md., and Georgia Reproductive Specialists, Atlanta, Ga.) was observed.

The zona pellucida was removed by 0.5% pronase (Sigma, St. Louis) treatment. The ICM from blastocysts was isolated by immuno-surgery where the blastocysts were incubated with horse antiserum to human spleen cells followed by exposure to guinea pig complement. Trophoectodern cells were removed from the ICM by gently pipetting the treated blastocysts.

For the derivation of ICM from whole blastocysts, the blastocysts were placed on a feeder layer in medium designed for culture of phESC (i.e., VitroHES™ media, e.g., DMEM/high glucose medium, VitroLife, Sweden) supplemented with 10% human umbilical cord blood serum, 5 ng/ml human recombinant LIF (Chemicon Intl, Inc., Temecula, Calif.), 4 ng/ml recombinant human FGF (Chemicon Intl, Inc., Temecula, Calif.) and penicillin-streptomycin (100 U/100 μg)). When blastocysts attached and trophoplast cells spread, the ICM became visible. Through three to four days of additional culture, the ICM was isolated through mechanical slicing of the ICM from the trophoectoderm outgrowth using a finely drawn glass pipette. Further, the IMC cells were cultured on a feeder cell layer of mitotically inactivated post natal human dermal fibroblasts, in VirtroHES™ media (as formulated above) in a 96-well plate in 5% CO₂ and 20% O₂ at 37° C. This gas mixture was used to culture stem cells. Human fibroblast cultures were made using non-animal materials. Inactivation of fibroblasts was carried out using 10 μg/ml mitomycin C (Sigma, St. Louis, Mo.) for 3 hours.

In a separate method, immuno-surgery was performed by incubating blastocysts with horse antiserum to human spleen cells followed by exposure to rabbit complement. The trophectoderm cells were removed from the ICM through gentle pipetting of the treated blastocyts. Further culturing of the isolated ICMs was performed on a feeder layer of neonatal human skin fibroblasts (HSF) obtained from a genetically unrelated individual (with parental consent) derived using medium containing human umbilical cord blood serum. The HSF feeder layer was mitotically inactivated using mitomycin C.

The medium for the culture of HSF consisted of 90% DMEM (high glucose, with L-glutamaine (Invitrogen), 10% human umbilical cord blood serum and penicillin-streptomycin (100 U/100 mg) Invitrogen).

For the culture of ICM and phESC, VitroHES™ (Vitrolife) supplemented with 4 ng/ml hrbFGF, 5 ng/ml hrLIF and 10% human umbilical cord blood serum was used. The ICM was mechanically plated on a fresh feeder layer and cultured for three to four days. The first colony was mechanically cut and replated after five days of culture. All subsequent passages were made after five to six days in culture. For early passages, colonies were mechanically divided into clumps and replated. Further passing of phESC was performed with collagenase IV treatment and mechanical dissociation. The propagation of phESC was performed at 37° C., 5% CO₂ in a humidified atmosphere.

Oocyte Activation

From the initial donor, four oocytes were activated, and the activated oocytes were cultivated in IVF medium in a gas environment comprising 5% 02, 5% CO₂, and 90% N₂ and followed over five (5) days. Table 2 shows the progress of maturation of the activated oocytes. Each oocyte was separated in a 4-well plate.

TABLE 2 Cultured Activated Oocytes* Day 1 Day 2 Day 3 Day 5 N1 1 pronucleus 2 blastomers 4 bl equal, 1 morula, (pn), (bl) equal, fr-2% fr-15% 1 polar body fragmentation (pb) (fr)-0% N2 0 pn, 4 bl not equal, 5 bl not equal, 4 bl not equal, 1 pb fr-4% fr-20% fr-40% N3 1 pn, 2 bl not equal, 6 bl equal, early 1 pb fr-0% fr-0% blastocysts N4 1 pn, 4 bl equal, 4 bl equal, Fully expanded 1 pb fr-10% fr-20% blastocyst with good ICM 1AA *Cells were incubated in M1 ™ media (MediCult) on the first day and M2 ™ media (MediCult) on days 2-5. Media was changed everyday. M1 ™ and M2 ™ contain human serum albumin, glucose and derived metabolites, physiological salts, essential amino acids, non-essential amino acids, vitamins, nucleotides, sodium bicarbonate, streptomycin (40 mg/l), penicillin (40.000 IU/l) and phenol red.

Inner cell masses were isolated from N4 and transferred to human fibroblast feeder cells as outlined above. N1 and N2 degenerated on Day 6. Further, on Day 6, N3 produced fully expanded blastocyst with ICM 2AB. N3 was then transferred to human fibroblast feeder cells on Day 6. ICM from N4 was unchanged. N3 was used to isolate stem cells.

ICM cells were cultivated in VitroHES™ medium in a gas environment comprising 5% CO₂, and 95% N₂ and followed over forty-five (45) days. Table 2a shows the progress of N3 ICM cell cultivation.

TABLE 2a Progress of N3-ICM Cultivation* Day 3 ICM transplanted on fresh feeder cells. Day 8 Colony of cells divided mechanically into 6 pieces and cultivated in 3 wells of a 96-well plate-1st passage. Day 14 From five (5) colonies of 1st passage, cells were mechanically divided, and 20 colonies of a 2nd passage were cultivated in 3 wells of a 24-well plate. Day 20 Cells were plated in 35 mm dish-3rd passage. Day 24 Five (5) 35 mm dishes were seeded with cells-4th passage. One dish was divided chemically with 5% pronase (Sigma) at room temperature. Day 30 Twenty-five (25) 35 mm were seeded with cells-5th** passage. Day 34 6th** cell passage. Day 35 11 ampules were frozen from the 6th passage. Day 37 7th** cell passage. Day 44 12 ampules were frozen from the 7th passage. Day 45 8th cell passage. *Cells were grown on M2 ™ media (MediaCult). **These passages were made with pronase digestion.

Stem Cell Isolation.

From the oocytes from 5 donors, the use of MediCult media followed by a culture under reduced oxygen allowed for the production of 23 blastocysts on the fifth or sixth day of culture. Eleven of the blastocysts had visible ICMs (Table 3).

TABLE 3 Generation of Parthenotes and Parthenogenetic Embryonic Stem Cell Lines Blastocysts derived Normally Without Donor Oocytes Oocytes activated Parthenotes With visible Lines Number harvested donated oocytes created ICM ICM generated 1 8 4 4 4 2 — phESC-1 immunosurgery 2 15 8 8 8 3 3 phESC-3 phESC-4 phESC-5 all from whole blastocysts 3 27 14  12¹ 11² 3 2 phESC-6 from whole blastocysts 4 22 11  10³ 10  2 3 phESC-7 from whole blastocysts 5 20  9⁴ 7 7 1 4 No cell line generated ¹two oocytes were not activated; ²one oocyte degenerated after activation; ³one oocyte was not activated; ⁴two oocytes were at metaphase stage I and were discarded.

These results indicate an approximate 57.5% success rate in the formation of blastocysts from parthenogenetically activated oocytes.

Immunohistochemical Staining

For immunostaining, hES cell colonies and phESC cells on feeder layers were seeded onto micro cover glass, washed twice with PBS and fixed with 100% methanol for 5 minutes at −20° C. Cells were washed twice with PBS+0.05% Tween-20 and permeabilized with PBS+0.1% Triton X-100 for 10 minutes at room temperature. After cell washing, non-specific binding was blocked by incubation with blocking solution (PBS+0.05% Tween-20+four percent goat serum plus three percent human umbilical cord blood serum) for 30 minutes at room temperature (RT). Monoclonal antibodies were diluted in blocking solution and used for one hour at RT: SSEA-1 (MAB4301) (1:30), SSEA-3 (MAB4303) (1:10), SSEA-4 (MAB4304) (1:50), OCT-4 (MAB4305) (1:30), TRA-1-60 (MAB4360) (1:50), and TRA-1-81 (MAB4381) (1:50) from Chemicon. After the cells were washed, secondary antibodies Alexa Fluor 546 (orange-fluorescent) and 488 (green-fluorescent) (Molecular Probes, Invitrogen) were diluted 1:1000 in PBS+0.05% Tween-20 and applied for one hour at RT. Cells were washed and nuclei were stained with DAPI (Sigma) 0.1 μg/ml in PBS+0.05% Tween-20 during ten minutes at RT. Cells were washed and mounted on slides with Mowiol (Calbiochem). Fluorescence images were visualized with a fluorescence microscope.

For the detection of mesodermal markers in three week old embryoid bodies or in contractile embryoid bodies, monoclonal mouse anti-desmina antibody anti-human alpha actinin antibody (Chemicon) as the muscle specific markers, and anti-human CD31/PECAM-1 antibody (R&D Systems), antihuman VE Cadherin (DC144) antibody (R&D Systems) as the endothelial markers were used.

For detection of the endodermal markers in embryoid bodies, monoclonal mouse anti-human alpha-fetoprotein antibody (R&D Systems) was used.

Alkaline Phosphatase and Telomerase Activity

Alkaline phosphatase and telomerase activity were performed according to the manufacturer's specifications with AP kit and TRAPEZE™ Kit (Chemicon).

Karyotyping

To analyse the karyotype, hES cells were treated with 10 μg/ml Demecolcine (Sigma) for two hours, harvested with 0.05% trypsin/EDTA (Invitrogen) and centrifuged at 700×rpm for three minutes. The pellet was resuspended in 5 ml of 0.56% KCl, and incubated for 15 minutes at RT. After repeated centrifugation, the supernatant was removed and cells were resuspended and fixed with 5 ml of an ice cold mixture of methanol/acetic acid (3:1) for five minutes at +4° C. The fixation of the cells was repeated twice, after that the cell suspension was placed onto microscope slides and the preparations were stained with Giemsa Modified Stain (Sigma). Metaphases from cells prepared in this manner were analyzed by a standard G-banding method. Quantity of 5/1000 metaphase spreads were revealed and 63 metaphases were analyzed.

Embryoid Body Formation

hES and phESC cell colonies were mechanically divided into clumps and placed in wells of a 24 well plate precoated with 1.5% agarose (Sigma) in medium containing 85% Knockout DMEM, 15% human umbilical cord blood serum, 1×MEM NEAA, 1 mM Glutamax, 0.055 mM β-mercaptoethanol, penicillin-streptomycin (50 U/50 mg), 4 ng/ml hrbFGF (all from Invitrogen, except serum). Human EBs were cultured for 14 days in suspension culture and placed on a culture dish to give outgrowth or cultivated in suspension for an additional week.

Neural differentiation was induced by the cultivation of two week old embryoid bodies attached to a culture dish surface over a period of a week in differentiation medium: DMEM/F12, B27, 2 mM Glutamax, penicillin-streptomycin (100 U/100 μg) and 20 ng/ml hrbFGF (all from Invitrogen). Some embryoid bodies gave rise to differentiated cells with neural morphology, others were dissected and additionally cultured to produce neurospheres.

Rhythmically beating embryoid bodies appeared spontaneously following five days of culture after plating on an adhesive surface in the same medium as was used for embryoid body generation.

HLA Typing

Genomic DNA was extracted from donor blood, hES, phESC cells, and human newborn skin fibroblasts (NSFs) with Dynabeads DNA Direct Blood from Dynal (Invitrogen). HLA typing was performed by PCR with allele-specific sequencing primers (PCR-SSP, Protrans) according to the manufacturer's specifications. HLA class I genes (HLA A*,B*,Cw*) were typed with PROTRANS HLA A* B* Cw* defining A*01-A*80, B*07-B*83, Cw*01-Cw*18 regions. HLA class II genes (HLA DRB1*, DRB3*, DRB4*, DRB5*, DQA1*, DQB1*) were analyzed with PROTRANS HLA DRB1* defining DRB1*01-DRB1*16 (DR1-DR18), DRB3*, DRB4*, DRB5* regions and PROTRANS HLA DQB1* DQA1* defining DQB1*02-DQB1*06 (DQ2-DQ9), DQA1*0101-DQA1*0601 regions. PCR amplification was achieved: at 94° C. for 2 min; 10 cycles at 94° C. for 10 sec, 65° C. for 1 min; 20 cycles at 94° C. for 10 sec, 61° C. for 50 sec, 72° C. for 30 sec. Amplified products were detected in 2% agarose gel.

Affimetrix SNP Microarray Analysis

Genomic DNA was isolated from blood, cumulus cells, phESC and NSF by phenol/chloroform extraction method. These DNA samples obtained from four Caucasian subjects were genotyped with Affimetrix Mapping 50K Hind 240 Array (part of Affimetrix GeneChip Mapping 100K kit). Initially, the dataset contained 57,244 binary SNP markers. Since the number of markers is more than would be necessary to identify the equivalency of genomic samples and to study heterozygosity, 15 (chromosomes 1-15) out of 22 autosomal chromosomes were chosen. The shorter seven chromosomes were removed to reduce the chance that no marker, or only a single marker for a given chromosome, is selected during random sampling. The 1,459 markers were analyzed by Relcheck (version 0.67, Copyright © 2000 Karl W. Broman, Johns Hopkins University, Licensed under GNU General Public License version 2 (June 1991)).

Genomic Imprinting Analysis

Total nucleic acid was prepared as described Li et al. (J Biol Chem (2002) 277(16):13518-13527). RNA and DNA were extracted from cells using Tri-reagent (Sigma) or by using an RNA preparation kit from Qiagen (Valencia, Calif.).

Northern blots containing RNA from the various samples (see FIG. 3) were blotted onto filters by standard methods (See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 1989, 2nd ed, Cold Spring Harbor Press). The Northern filter was hybridized with single stranded oligonucleotide probes that hybridized specifically to the mRNAs. The oligonucleotide probes were end-labeled with [γ³²P]ATP (Amersham Biosciences). The filters were subsequently washed three times for 10 min each with 0.2×SSC (1×SSC=0.15 M NaCl and 0.015 M sodium citrate) containing 0.1% SDS at 60° C. and analyzed by PhosphorImager (Molecular Dynamics). The sequences of the oligonucleotide probes were obtained from sequences based on the following Accession Nos.: NP002393 (Peg1_2 and Peg1_A; for these genes, human PEG1 is transcribed from two alternative promoters, resulting in the transcription of two isoforms, of which only one (isoform 1_2) is imprinted. Paternal expression isoform 1 occurs in conjunction with an unmethylated CpG island in exon 1 of the paternal allele, whereas the corresponding CpG island in the maternal gene (isoform 1_A) is fully methylated. See, e.g., Li et al. (2002), supra); CAG29346 (SNRPN); AF087017 (H19); NR 001564 (inactive X specific transcripts-XIST); and P04406 (GAPDH).

DNA Fingerprinting Analysis

Genomic DNA was isolated from blood, hES cells, and NSFs through a phenol/chloroform extraction, digested with HinfI restriction enzyme (Fermentas) and loaded in a 0.8% agarose gel. Following electrophoresis, denatured DNA was transferred to a nylon membrane (Hybond N, Amersham) by Southern blotting and hybridized with ³²P-labeled (CAC) 5 oligonucleotide probe. mData were analyzed after membrane exposition on X-ray film (Kodak XAR) using Cronex intensifying screens.

Monolocus PCR Genotyping

In order to determine allelic identities for minisatellite loci between blood donor DNA and stem cell DNA, 11 polymorphic sites ((1) 3′ Apolipoprotein B hypervariable minisatellite locus (3′ApoB); (2) D1S80 (PMCT118) hypervariable minisatellite locus (D1S80); (3) D6S366; (4) D165359; (5) D7S820; (6) Human von Willebrand factor gene hypervariable minisatellite locus II (vWFII); (7) D135317; (8) Human von Willebrand factor gene hypervariable microsatellite locus (vWA); (9) Human c-fms proto-oncogene for CFS-1 receptor gene microsatellite locus (CSF1PO); (10) Human thyroid peroxidase gene microsatellite locus (TPDX); and (11) Human tyrosine hydroxylase gene microsatellite locus (TH01)) were analyzed by PCR genotyping. Allele frequencies for known populations (i.e., Russian and Caucasian-American populations) determined for the above polymorphic sites were compared to allele frequencies of these sites in test samples (i.e., hES, NSF, and donor blood DNA). Chromosomal location, Genbank locus and locus definition, repeat sequence data, allelic ladder range, VNTR ladder size range, other known alleles, allele sizes, PCT Protocols, and allele frequency results for the 11 minisatellite loci of the disclosed populations analyzed are provided below.

(1) 3′ Apolipoprotein B Hypervariable Minisatellite Locus (3′ApoB VNTR)

Chromosomal location: 2p23-p23

GenBank locus and locus definition: APOB, apolipoprotein B (including Ag(x) antigen) untranslated region

  Repeat sequence 5′-3′: (SEQ ID NO: 1) (TATAATTAAATATTTTATAATTAAAATATT)n

Allelic ladder size range (bases): 450+10+2 primer+links

VNTR ladder size range (# of repeats, according to Ludwig et al, 1989): 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52

Other known alleles (# of repeats): 25, 27, 28, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 54, 55

Promega K562 DNA® Allele sizes (# of repeats): 36/36

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 1′ Elongation and primer linking 60° C., 2′ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time The analysis may be done as described in Verbenko et al. (Apolipoprotein B 3′-VNTR polymorphism in Eastern European populations. Eur J Hum Gen (2003) 11(1):444-451). See Table 4.

TABLE 4 Allele Frequencies for Russian Populations Allele Allele frequency Number of Alleles observed 25 0.001 1 30 0.079 75 32 0.071 68 33 0.001 1 34 0.238 227 35 0.004 4 36 0.393 375 37 0.001 1 38 0.036 36 39 0.001 1 40 0.014 13 42 0.001 1 44 0.042 41 45 0.006 6 46 0.033 31 48 0.067 64 50 0.011 10 52 0.001 1 Homozygotes 94 Heterozygotes 333 Total samples 427

(2) D1S80 (pMCT118) Hypervariable Minisatellite Locus (D1S80 VNTR)

Chromosomal location: 1p35-36

GenBank locus and locus definition: Human D1S80 and MCT118 gene

Repeat sequence 5′-3′: (GAAGACAGACCACAG)n (SEQ ID NO: 2)

Allelic ladder size range (bases): 387-762

VNTR ladder size range (# of repeats): 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41

Other known alleles (# of repeats): 13, 14, 15, 38, 39, >41

Promega K562 DNA® Allele sizes (# of repeats): 18/29

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 60° C., 30″ Elongation 72° C., 45″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis may be done as described in Verbenko et al. (Allele frequencies for D1S80 (pMCT118) locus in some Eastern European populations. J Forensic Sci (2003) 48(1):207-208). See Table 5.

TABLE 5 Allele Frequencies for Russian Populations Allele Allele frequency Number of Alleles observed 18 0.280 33 20 0.017 2 21 0.009 1 22 0.042 5 23 0.017 2 24 0.390 46 25 0.017 2 26 0.025 3 28 0.068 8 29 0.009 1 30 0.034 4 31 0.059 7 33 0.017 2 34 0.008 1 36 0.008 1 Homozygotes 15 Heterozygotes 44 Total samples 59

(3) D6S366

Chromosomal location: 6q21-qter

GenBank locus and locus definition: NA

Allelic ladder size range (bases): 150-162

STR ladder size range (# of repeats): 12, 13, 15

Other known alleles (# of repeats): 10, 11, 14, 16, 17

Promega K562 DNA® Allele sizes (# of repeats): 13/14

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 1′ Elongation and primer linking 60° C., 2′ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis may be done as described in Efremov et al. (An expert evaluation of molecular genetic individualizing systems based on the HUMvWFII and D6S366 tetranucleotide tandem repeats. Sud Med Ekspert (1998) 41(2):33-36). See Table 6.

TABLE 6 Allele Frequencies for Russian Populations Allele Allele frequency Number of Alleles observed 10 0.008 3 11 0.059 21 12 0.316 112 13 0.251 89 14 0.085 30 15 0.175 62 16 0.015 7 17 0.011 4 Total samples 177

(4) D16S539

Chromosomal location: 16q24-qter

GenBank locus and locus definition: NA

Repeat sequence 5′-3′: (AGAT)n

Allelic ladder size range (bases): 264-304

STR ladder size range (# of repeats): 5, 8, 9, 10, 11, 12, 13, 14, 15

Promega K562 DNA® Allele sizes (# of repeats): 11/12

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 64° C., 30″ Elongation 72° C., 30″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 7.

TABLE 7 Allele Frequencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 6 0.000 0 7 0.000 0 8 0.026 11 9 0.107 45 10 0.079 33 11 0.319 134 12 0.269 113 13 0.167 70 14 0.031 13 15 0.002 1 Homozygotes 57 Heterozygotes 153 Total samples 210

(5) D7S820

Chromosomal location: 7q11.21-22

GenBank locus and locus definition: NA

Repeat sequence 5′-3′: (AGAT)n

Allelic ladder size range (bases): 215-247

VNTR ladder size range (# of repeats): 6, 7, 8, 9, 10, 11, 12, 13, 14

Promega K562 DNA® Allele sizes (# of repeats): 9/11

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 64° C., 30″ Elongation 72° C., 30″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 8.

TABLE 8 Allele Frequencies for D7S820 in Different Populations Allele frequency Number of Allele Number of for Caucasian- Alleles frequency Alleles Allele Americans observed for Russians observed 6 0.002 1 0.0012 1 7 0.010 4 0.0087 7 8 0.155 65 0.1928 155 9 0.152 64 0.1480 119 10 0.295 124 0.2524 203 11 0.195 82 0.2040 164 12 0.121 51 0.1580 127 13 0.057 24 0.0299 24 14 0.012 5 0.0050 4 Homozygotes 43 92 Heterozygotes 167 310 Total samples 210 402

(6) Human Von Willebrand Factor Gene Hypervariable Microsatellite Locus II (vWFII)

Chromosomal location: 12p13.3-12p13.2

GenBank locus and locus definition: HUMvWFII, Human von Willebrand factor gene

Repeat sequence 5′-3′: (ATCT)n/(AGAT)n

Allelic ladder size range (bases): 154-178

STR ladder size range (# of repeats): 9, 11, 12, 13

Other known alleles (# of repeats): 8, 10, 14, 15

Promega K562 DNA® Allele sizes (# of repeats): 13/13

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 1′ Elongation and primer linking 60° C., 2′ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in Efremov et al. (An expert evaluation of molecular genetic individualizing systems based on the HUMvWFII and D6S366 tetranucleotide tandem repeats. Sud Med Ekspert (1998) 41(2):33-36). See Table 9.

TABLE 9 Allele Frequencies for Russian Populations Allele Allele frequency Number of Alleles observed 9 0.082 37 10 0.088 40 11 0.392 177 12 0.296 134 13 0.069 31 14 0.058 26 15 0.015 7 Total samples 226

(7) D135317

Chromosomal location: 13q22-q31

GenBank locus and locus definition: NA

Repeat sequence 5′-3′: (AGAT)n

Allelic ladder size range (bases): 165-197

STR ladder size range (# of repeats): 8, 9, 10, 11, 12, 13, 14, 15

Other known alleles (# of repeats): 7

Promega K562 DNA® Allele sizes (# of repeats): 8/8

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 64° C., 30″ Elongation 72° C., 30″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 10.

TABLE 10 Allele Frequencies for D13S317 in Different Populations Allele frequency Number of Allele Number of for Caucasian- Alleles frequency Alleles Allele Americans observed for Russians observed 7 0.000 0 0 0 8 0.143 60 0.1393 112 9 0.052 22 0.0883 71 10 0.052 22 0.0684 55 11 0.305 128 0.3706 298 12 0.307 129 0.2040 164 13 0.083 35 0.0871 70 14 0.057 24 0.0423 34 15 0.000 0 0 0 Homozygotes 61 90 Heterozygotes 149 312 Total samples 210 402

(8) Human Von Willebrand Factor Gene Hypervariable Microsatellite Locus (vWA)

Chromosomal location: 12p12pter

GenBank locus and locus definition: HUMVWFA31, Human von Willebrand factor gene

Repeat sequence 5′-3′: (AGAT)n

Allelic ladder size range (bases): 139-167

STR ladder size range (# of repeats): 14, 16, 17, 18

Other known alleles (# of repeats): 11, 12, 13, 15, 19, 20, 21

Promega K562 DNA® Allele sizes (# of repeats): 16/16

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 1′ Elongation and primer linking 60° C., 2′ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 11.

TABLE 11 Allele Frequencies for HUMVWFA31 in Different Populations Allele frequency Number of Allele Number of for Caucasian- Alleles frequency Alleles Allele Americans observed for Russians observed 13 0.000 0 0.0025 2 14 0.131 56 0.0796 64 15 0.082 35 0.0920 74 16 0.211 90 0.2127 171 17 0.265 113 0.2836 228 18 0.202 86 0.2251 181 19 0.087 37 0.0833 67 20 0.021 9 0.0199 16 21 0.000 0 0.0012 1 Homozygotes 38 70 Heterozygotes 175 332 Total samples 213 402

(9) Human c-Fms Proto-Oncogene for CSF-1 Receptor Gene Microsatellite Locus (CSF1PO)

Chromosomal location: 5q33.3-34

GenBank locus and locus definition: HUMCSF1PO, Human c-fms proto-oncogene

Repeat sequence 5′-3′: (AGAT)n

Allelic ladder size range (bases): 295-327

STR ladder size range (# of repeats): 7, 8, 9, 10, 11, 12, 13, 14, 15

Other known alleles (# of repeats): 6

Promega K562 DNA® Allele sizes (# of repeats): 9/10

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 64° C., 30″ Elongation 72° C., 30″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 12.

TABLE 12 Allele Frequencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 6 0.000 0 7 0.000 0 8 0.002 1 9 0.033 14 10 0.251 108 11 0.309 133 12 0.330 142 13 0.060 26 14 0.014 6 15 0.000 0 Homozygotes 47 Heterozygotes 168 Total Samples 215

(10) Human Thyroid Peroxidase Gene Microsatellite Locus (TPDX)

Chromosomal location: 2p25.1-pter

GenBank locus and locus definition: HUMTPDX, Human thyroid peroxidase gene

Repeat sequence 5′-3′: (AATG)n

Allelic ladder size range (bases): 224-252

STR ladder size range (# of repeats): 6, 7, 8, 9, 10, 11, 12, 13

Other known alleles (# of repeats): none

Promega K562 DNA® Allele sizes (# of repeats): 8/9

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 64° C., 30″ Elongation 72° C., 30″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 13.

TABLE 13 Allele Frequencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 6 0.002 1 7 0.000 0 8 0.528 227 9 0.093 40 10 0.056 24 11 0.284 122 12 0.037 16 13 0.000 0 Homozygotes 76 Heterozygotes 139 Total samples 215

(11) Human Tyrosine Hydroxylase Gene Microsatellite Locus (TH01)

Chromosomal location: 5q33.3-34

GenBank locus and locus definition: HUMTHO1, Human tyrosine hydroxylase gene

Repeat sequence 5′-3′: (AATG)n

Allelic ladder size range (bases): 179-203

STR ladder size range (# of repeats): 5, 6, 7, 8, 9, 10, 11

Other known alleles (# of repeats): 9.3

Promega K562 DNA® Allele sizes (# of repeats): 9.3/9.3

PCT Protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95° C., 2′ Cycling for 30 cycles: Denaturation 94° C., 45″ Primer linking 64° C., 30″ Elongation 72° C., 30″ Extension step: 72° C., 5′ Hold step:  4° C., unlimited time

The analysis has been done as described in GenePrint® STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, Wis. USA: 1993-2001. See Table 14.

TABLE 14 Allele Frequencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 5 0.007 3 6 0.237 101 7 0.148 63 8 0.117 50 9 0.155 66 9.3 0.331 141 10 0.005 2 11 0.000 0 Homozygotes 50 Heterozygotes 163 Total samples 213

Results

The hES cells from this method display many features that are typical for embryonic stem cells: cytoplasmic lipid bodies, small cytoplasmic/nuclear ratio and clearly distinguishable nucleoli. The hES cell colonies display similar morphology to that reported previously for human embryonic stem cells derived after in vitro fertilization. The cells were immunoreactively positive for alkaline phosphatase (FIG. 1A), octamer-binding transcription factor 4 mRNA (Oct-4) (FIG. 1B), stage-specific embryonic antigen 1 (SSEA-1) (FIG. 1C), stage-specific embryonic antigen 3 (SSEA-3) (FIG. 1D), stage-specific embryonic antigen 4 (SSEA-4) (FIG. 1E), tumor rejection antigen 1-60 (TRA-1-60) (FIG. 1F), tumor rejection antigen 1-81 (TRA-1-81) (FIG. 1G), and negative for stage-specific embryonic antigen 1 (SSEA-1) (FIG. 1C), (which is positive for mouse embryonic stem cells, but not for human). Telomerase activity is often correlated with replicative immortality and is typically expressed in germ cells, cancer cells, and a variety of stem cells, including stem cells, but absent in most somatic cell types. The cells prepared by this method after three months in in vitro proliferation maintained their undifferentiated morphology and displayed high levels of telomerase activity (FIG. 2A). The pluripotency of the cells was investigated in vitro by embryoid body formation (FIG. 2B, 2C), G-banded karyotyping shows that cells have normal human 46XX karyotype (FIG. 2D).

DNA fingerprinting analysis was performed on the blood of the oocyte donor, on the ES cells, and on the HNSF feeder cells by Southern blotting and hybridization with a ³²P-labeled (CAC)s oligonucleotide probe (FIG. 2E), and monolocus polymerase chain reaction (PCR) with different locuses.

For monolocus PCR, genotyping revealed identical alleles for all loci (but one, D7S820) between blood (donor) DNA and OL1 DNA. See Table 15.

TABLE 15 Monolocus PCR Genotyping Locus Chromosomal NN definition location hES NSF Blood 1. 3′ApoB 2p24-p23 36/48 36/36 36/48 2. D1S80 1p35-36 18/24 22/31 18/24 3. D6S366 6q21-qter 13/15 17/17 13/15 4. D16S359 16q24-qter  8/13 12/13  8/13 5. D7S820 7q11.21-22 11/11  9/10 10/11 6. vWFII 12p13.3-12p13.2 11/13  9/11 11/13 7. D13S317 13q22-q31  9/12 11/12  9/12 8. vWA 12p12pter 14/18 17/18 14/18 9. CSF1PO 5q33.3-34 12/12 12/13 12/12 10. TPOX 2p25.1-pter  8/11  8/11  8/11 11. TH01 5q33.3-34 6/6  6/9, 3 6/6

Heterozygosity (heterozygosis) of all heterozygous donor loci (but one, D7S820) was not changed in hES loci. Homozygosity (homozygosis) of D7S820 locus in hES DNA is a result of mutation (insertion of one AGAT monomer in microsatellite repeat) due to slipped-strand mispairing during DNA replication and DNA repair.

These results are in accordance with those obtained with multilocus DNA fingerprinting (when substantially identical fingerprint patterns for donor DNA and hES DNA were found).

FIG. 2E demonstrated heterozygosity of hES cells and their identity with the oocyte donor's blood, and there was no similarity between the hES cells and the feeder cells. The DNA profile of hES cell line was confirmed by PCR-based haplotype analysis using polymorphic genes within the MHC class I and class II. Total genomic DNA from the oocyte donor blood cells, from hES cells, and feeder HNSFs were genotyped and compared. The data demonstrated that hES cells and cells from donor blood were indistinguishable from each other and therefore should be considered autologous, and both distinguished from DNA of the feeder cells (Table 16).

TABLE 16 HLA Typing MHC I MHC II HLA-A HLA-B HLA-C DRB1 DQB1 DQA1 pHES-1 A*01 B*15(63) Cw*04 DRB1*12 DQB1*06 DQA1*01 A*02 B*35 Cw*0708 DRB1*13 DQB1*03 DQA1*0505 Donor A*01 B*15(63) Cw*04 DRB1*12 DQB1*06 DQA1*01 A*02 B*35 Cw*0708 DRB1*13 DQB1*03 DQA1*0505 HNSF A*25 B*15(62) Cw*12 DRB1*04 DQB1*06 DQA1*01 A*32 B*18 Cw*12 DRB1*15 DQB1*03 DQA1*03

DNA fingerprinting and HLA typing analysis confirmed that the hES cells are heterozygous and contain the whole donor genetic material. These results coincide with data from parthenogenetic monkey stem cell lines (Vrana et al., Proc Natl Acad Sci USA (2003) 100(Suppl 1):11911-11916), and do not coincide with data from parthenogenetic mouse stem cell lines (Lin et al., Stem Cells (2003) 21:153-161), which contains half of the donor genetic material.

The phESC lines display a morphology expected in hES cells, forming colonies with tightly packed cells, prominent nucleoli and a small cytoplasm to nucleus ratio (FIG. 4). These cells express traditional hES markers SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, and OCT-4, and do not express SSEA-1, a positive marker for undifferentiated mouse embryonic stem cells (FIG. 4). The cells derived from all lines demonstrate high levels of alkaline phosphatase and telomerase activity (FIG. 5 and FIG. 6). G-banded karyotyping showed that phESC lines have a normal human 46,XX karyotype, with the exception of the phESC-7 line (FIG. 7). Approximately 91% of cells from the phESC-7 line have a 47,XXX karyotype and 9% of the cells have a 48,XXX,+6 karyotype. A different degree of X chromosome heteromorphism was observed in the lines; approximately 12% of the phESC-1 and phESC-6 lines; 42% for the phESC-5 line; and 70, 80, and 86% for the cell lines phESC7, phESC-3, and phESC-4, respectively (FIG. 7).

Comparative DNA profiling of was performed on all the phESC lines, the donor somatic cells and the feeder cells. These studies used Affimetrix SNP microarrays (Mapping 50K Hind 240 Arrays) to study chromosome changes and to confirm the genetic similarity of the phESC to the donor's somatic cells. All paired genotype relationships between phESC lines and their associated donor somatic cells were identified as “full siblings”, and all other combinations of pairs were identified as “unrelated”. Internal controls identified the paired genotype relationship between split cultures derived from the same phESC line as “monozygotic twins” (Table 17, Database S1).

TABLE 17 Database S1 Database S1 Identifying DNA samples from phESC and related donors putative inferred LOD LOD LOD LOD genotype 1 genotype 2 relationship relationship IBS 0 IBS 1 IBS 2 n_typed MZtwins par/off fullsibs halfsibs unrelated 1 2 unrelated unrelated 166 662 631 1459 −1503.03 −300.45 −23.15 −8.41 0 1 3 unrelated unrelated 241 616 602 1459 −1560.65 −434.85 −28.04 −12.22 0 1 4 unrelated unrelated 225 623 611 1459 −1535.94 −400.61 −31.39 −14.39 0 1 5 unrelated unrelated 225 623 611 1459 −1535.94 −400.61 −31.39 −14.39 0 1 6 unrelated unrelated 243 644 572 1459 −1642.35 −445.78 −31.74 −14.54 0 1 7 unrelated unrelated 252 638 569 1459 −1641.11 −453.5 −29.25 −12.86 0 1 8 unrelated unrelated 250 643 566 1459 −1656.02 −460.02 −32.86 −15.32 0 1 9 unrelated unrelated 219 657 583 1459 −1605.31 −382.39 −27.37 −11.58 0 1 10 unrelated unrelated 158 707 594 1459 −1591.43 −279.21 −26.37 −10 . . . 89 0 1 11 unrelated unrelated 193 668 598 1459 −1584.71 −354.76 −29.65 −13 . . . 31 0 1 12 unrelated unrelated 166 671 622 1459 −1523.1 −300.5 −30.53 −13 . . . 92 0 2 3 unrelated full sibs 0 282 1177 1459 −440.02 −146.3 0 −167.42 −363.63 2 4 unrelated unrelated 233 627 599 1459 −1569.66 −423.24 −28.24 −12.91 0 2 5 unrelated unrelated 233 627 599 1459 −1569.66 −423.24 −28.24 −12.91 0 2 6 unrelated unrelated 217 650 592 1459 −1584.75 −388.44 −22.62 −8.53 0 2 7 unrelated unrelated 243 650 566 1459 −1645.94 −437.91 −23.23 −8.72 0 2 8 unrelated unrelated 225 649 585 1459 −1603.18 −404.41 −27.04 −11.97 0 2 9 unrelated unrelated 210 639 610 1459 −1532.75 −360.46 −24.72 −9.89 0 2 10 unrelated unrelated 144 683 632 1459 −1491.18 −243.56 −16.82 −4.51 0 2 11 unrelated unrelated 172 680 607 1459 −1556.46 −310.03 −23.5 −9.7 0 2 12 unrelated unrelated 176 667 616 1459 −1538.57 −327.95 −27.31 −12 . . . 06 0 3 4 unrelated unrelated 336 457 666 1459 −1391.57 −599.92 −30.6 −14.62 0 3 5 unrelated unrelated 336 457 666 1459 −1391.57 −599.92 −30.6 −14.62 0 3 6 unrelated unrelated 322 482 655 1459 −1415.98 −571.23 −26.08 −11.86 0 3 7 unrelated unrelated 369 442 648 1459 −1432.05 −664.95 −27.39 −11.93 0 3 8 unrelated unrelated 334 483 642 1459 −1449.86 −597.75 −31.68 −15.14 0 3 9 unrelated unrelated 307 493 659 1459 −1395.19 −530.45 −24.56 −10 0 3 10 unrelated unrelated 215 623 621 1459 −1503.92 −364.97 −17.26 −4.43 0 3 11 unrelated unrelated 264 582 613 1459 −1531.91 −473.48 −28.41 −12 . . . 81 0 3 12 unrelated unrelated 254 595 610 1459 −1544.73 −460.57 −29.92 −13 . . . 88 0 4 5 unrelated MZ twins 0 0 1459 1459 0 −379.58 −45.47 −401.67 −677.74 4 6 unrelated unrelated 334 475 650 1459 −1436.59 −599.55 −32.73 −15.19 0 4 7 unrelated unrelated 365 439 655 1459 −1418.34 −656.01 −31.6 −14.56 0 4 8 unrelated unrelated 329 486 644 1459 −1450.75 −586.4 −32.06 −14.88 0 4 9 unrelated unrelated 332 466 661 1459 −1395.18 −590.12 −28.69 −12.94 0 4 10 unrelated unrelated 245 606 608 1459 −1542.32 −438.93 −28.75 −12 . . . 74 0 4 11 unrelated unrelated 273 569 617 1459 −1530.97 −492.84 −29.03 −12 . . . 34 0 4 12 unrelated full sibs 0 224 1235 1459 −326.17 −162.34 0 −183.44 −393.46 5 6 unrelated unrelated 334 475 650 1459 −1436.59 −599.55 −32.73 −15.19 0 5 7 unrelated unrelated 365 439 655 1459 −1418.34 −656.01 −31.6 −14.56 0 5 8 unrelated unrelated 329 486 644 1459 −1450.75 −586.4 −32.06 −14.88 0 5 9 unrelated unrelated 332 466 661 1459 −1395.18 −590.12 −28.69 −12.94 0 5 10 unrelated unrelated 245 606 608 1459 −1542.32 −438.93 −28.75 −12 . . . 74 0 5 11 unrelated unrelated 273 569 617 1459 −1530.97 −492.84 −29.03 −12 . . . 34 0 5 12 unrelated full sibs 0 224 1235 1459 −326.17 −162.34 0 −183.44 −393.46 6 7 unrelated full sibs 45 176 1238 1459 −277.78 −217.21 0 −165.72 −390.62 6 8 unrelated full sibs 44 187 1228 1459 −289.8 −201.32 0 −153.75 −365.51 6 9 unrelated unrelated 333 481 645 1459 −1436.5 −595.4 −30.3 −13.77 0 6 10 unrelated unrelated 240 601 618 1459 −1518.17 −425.03 −27.11 −11 . . . 53 0 6 11 unrelated full sibs 0 164 1295 1459 −209.27 −191.66 0 −213.25 −440.56 6 12 unrelated unrelated 234 615 610 1459 −1547.15 −416.14 −30.21 −13 . . . 64 0 7 8 unrelated full sibs 38 225 1196 1459 −326.62 −150.16 0 −121.55 −334.09 7 9 unrelated unrelated 359 473 627 1459 −1479.28 −642.41 −30.61 −14.47 0 7 10 unrelated unrelated 252 623 584 1459 −1598.35 −443.81 −28.88 −13 . . . 09 0 7 11 unrelated full sibs 0 230 1229 1459 −318.49 −137.93 0 −159.55 −389.58 7 12 unrelated unrelated 265 583 611 1459 −1539.33 −472.91 −30.55 −13 . . . 87 0 8 9 unrelated unrelated 347 480 632 1459 −1472.41 −625.68 −30.93 −14.31 0 8 10 unrelated unrelated 244 614 601 1459 −1561.3 −434 −28.07 −12 . . . 37 0 8 11 unrelated full sibs 0 175 1284 1459 −223.73 −178.56 0 −200.12 −428.04 8 12 unrelated unrelated 236 610 613 1459 −1539.08 −417.14 −29.32 −13 . . . 14 0 9 10 unrelated full sibs 0 228 1231 1459 −315.15 −152.88 0 −174.27 −392.91 9 11 unrelated unrelated 269 567 623 1459 −1502.69 −479.57 −28.47 −12 . . . 55 0 9 12 unrelated unrelated 245 612 602 1459 −1557.25 −438.53 −26.07 −11 . . . 15 0 10 11 unrelated unrelated 187 635 637 1459 −1478.7 −328.06 −25.52 −10.6 0 10 12 unrelated unrelated 181 662 616 1459 −1534.36 −329 −25.2 −10.6 0 DNA samples were numbered as follows: 1-human neonatal skin fibroblasts; 2-phESC-7 line donor; 3-phESC-7 line; 4-phESC-1 line; 5-phESC-1 line; 6-phESC-3 line; 7-phESC-4 line; 8-phESC-5 line; 9-phESC-6 line; 10-phESC-6 line donor; 11-phESC-3 to phESC-5 lines donor; and 12-phESC-1 line donor. The result shows that only one pair (sample 4-5), has been identified as monozygotic (MZ) twins. Ten other pairs (samples 2-3, 4-12, 5-12, 6-7, 6-11, 7-8, 7-11, 8-11, 9-10) have been identified as full siblings, and all the other combination of pairs have been identified as unrelated. The IBS columns in the output display the number of markers at which the pair are both typed and share 0, 1, or 2 alleles identical by state (For MZ twins under ideal conditions of no genotyping errors, all markers must be placed under IBS = 2). The output does not display P (observed markers | given relationship) directly, but it displays LOD score − log₁₀ {P(observed markers | putative relationship/P(observed markers | relationship for which maximum likelihood was obtained and thus the call was made)} as a measure of similarity. The smaller the LOD score is, the less likely the putative relationship between two samples it.

Comparative analysis of 1,459 SNP markers revealed phESC heterozygosity and showed that changes had occurred in the phESC cell genotype in comparison to the related donor somatic cell genotype. Some segments of the somatic cell genome that had formerly been heterozygous became homozygous in the related phESC line genome. This heterozygous to homozygous pattern occurred in 11-15% of the phESC-1, PhESC-3, phESC-4, phESC-5 and phESC-6 lines, and was 19% for the phESC7 line (Database S2). Moreover, genetic differences were observed between the phESC and phESC-5 lines that had been derived from the same oocyte donor (Table 18, Database S2).

TABLE 18 Database S2 Database S2 Heterozygosity of phESC (Abbreviated as “pC”) Lines chromo- RS ID basepair Freq A in pC-1 N3-5 pC-6 pC-7 some SNP ID (dbSNP) basepair (Mb) Caucasian pC-1 donor pC-3 pC-4 pC-5 donor pC-6 donor pC-7 donor 1 SNP_A- rs10752719 3744122 3.744122 0.436 AB AB BB AB AB AB BB BB BB BB 1697748 1 SNP_A- rs806104 5977200 5.9772 0.631 AB AB AA AB AB AB AB AB AA AA 1743594 1 SNP_A- rs301791 8402638 8.402638 0.274 AB AB BB BB BB BB AB AB AA AB 1687843 1 SNP_A- rs1474868 11978430 11.97843 0.333 BB BB AA AA AA AA AA AA AA AA 1647681 1 SNP_A- rs1417144 14211391 14.211391 0.548 AA AA AB AB AB AB AA AA AB AB 1673737 1 SNP_A- rs860379 18414756 18.414756 0.25 BB BB BB BB BB BB BB BB BB BB 1747116 1 SNP_A- rs10492997 19514677 19.514677 0.631 AA AA BB BB BB BB AB AB AA AA 1662223 1 SNP_A- rs559346 28077956 28.077956 0.583 BB AB AB AB AB AB AB AB AA AB 1662225 1 SNP_A- rs4949455 31783886 31.783886 0.382 AA AB AB BB AB AB AB AB AA AA 1646469 1 SNP_A- rs6661190 33872782 33.872782 0.274 BB BB BB BB BB BB BB BB BB AB 1695076 1 SNP_A- rs4653029 34558585 34.558585 0.274 BB BB BB BB BB BB BB BB BB BB 1679571 1 SNP_A- rs7531479 36798680 36.79868 0.714 AA AA AA AA AA AA AA AA AA AA 1675060 1 SNP_A- rs1010805 37858235 37.858235 0.738 AA AA AB AA BB AB AA AA BB BB 1753902 1 SNP_A- rs6693076 39972196 39.972196 0.441 AA AA AB AA BB AB AB AB BB BB 1691977 1 SNP_A- rs407752 40472948 40.472948 0.333 BB BB AB AA BB AB BB BB BB BB 1723259 1 SNP_A- rs7515340 41055964 41.055964 0.381 AB AB AA AA AA AA AA AA BB BB 1692103 1 SNP_A- rs4660575 41902429 41.902429 0.429 BB BB BB BB BB BB AA AA BB AB 1696731 1 SNP_A- rs1408412 42787470 42.78747 0.679 AA AA AA AA AA AA AA AA AA AA 1701070 1 SNP_A- rs1771551 45552736 45.552736 0.738 AA AA AA AA AA AA AA AA BB AB 1729559 1 SNP_A- rs2245122 47358015 47.358015 0.598 AA AA AA AA AA AA BB BB BB AB 1670587 1 SNP_A- rs1875645 50501900 50.5019 0.524 AB AB BB BB BB BB BB BB BB BB 1711898 1 SNP_A- rs625643 54349188 54.349188 0.25 BB BB BB BB BB BB BB BB BB BB 1645411 1 SNP_A- rs10493206 56531172 56.531172 0.488 AA AA BB BB BB BB AB AB AA AB 1718210 1 SNP_A- rs1831870 57339224 57.339224 0.524 AB AB AB AA BB AB BB BB BB AB 1752670 1 SNP_A- rs852766 57998529 57.998529 0.564 AA AA AA AA AA AA AA AA BB AB 1669308 1 SNP_A- rs1969772 58917123 58.917123 0.738 AA AA AA AA AA AA AB AB AA AB 1681141 1 SNP_A- rs10489908 61576784 61.576784 0.738 AA AA AA AA AA AA AA AA AA AA 1690420 1 SNP_A- rs2765249 62441479 62.441479 0.75 AA AA AA AA AA AA BB BB AA AB 1727043 1 SNP_A- rs3861943 63439667 63.439667 0.405 BB BB BB BB BB BB AB AB AA AB 1646105 1 SNP_A- rs592298 64000081 64.000081 0.25 BB BB BB BB BB BB AB AB BB AB 1654674 1 SNP_A- rs746633 64503887 64.503887 0.692 AA AA BB BB BB BB BB BB AA AB 1708628 1 SNP_A- rs1171279 65700514 65.700514 0.345 BB BB BB BB BB BB BB BB BB AB 1713897 1 SNP_A- rs1280310 66928844 66.928844 0.655 AB AB AB BB AA AB AB AB AA AB 1717648 1 SNP_A- rs1408956 67849084 67.849084 0.536 AB AB AB AA BB AB AB AB BB BB 1712508 1 SNP_A- rs1413953 70834525 70.834525 0.571 AB AB AA AA AA AA AB AB AA AB 1688631 1 SNP_A- rs1338655 73569634 73.569634 0.429 AB AB AA AA AA AA AA AA BB BB 1720162 1 SNP_A- rs10493539 74427598 74.427598 0.25 AA AA BB BB BB BB BB BB AA AB 1697494 1 SNP_A- rs277355 75002805 75.002805 0.345 BB BB BB BB BB BB AB AB BB AB 1649261 1 SNP_A- rs1250876 75905253 75.905253 0.345 AB AB AB BB AA AB AB AB BB BB 1744876 1 SNP_A- rs3928852 76926021 76.926021 0.607 AA AA AA AA AA AA AB AB AA AA 1739854 1 SNP_A- rs10493596 77438262 77.438262 0.718 AA AA AA AA AA AA AB AB AA AA 1687047 1 SNP_A- rs1248480 79071260 79.07126 0.357 BB BB AA AA AA AA AB AB BB BB 1732619 1 SNP_A- rs2127436 79792017 79.792017 0.488 AB AB AB BB AA AB BB BB AA AB 1664985 1 SNP_A- rs2389016 80511350 80.51135 0.738 AA AA AB BB AA AB AB AB AA AB 1644541 1 SNP_A- rs10518660 82094088 82.094088 0.738 AB AB AA AA AA AA AA AA AA AA 1645927 1 SNP_A- rs6598991 82697988 82.697988 0.524 BB BB AB AA AB AB AA AA AA AA 1693780 1 SNP_A- rs2268667 85505767 85.505767 0.321 BB BB AB AA AB AB BB BB BB AB 1674234 1 SNP_A- rs306322 88673430 88.67343 0.726 AA AA AA AA AA AA AB AB BB AB 1752288 1 SNP_A- rs1831298 90211840 90.21184 0.262 AB AB BB BB BB BB AA AA BB AB 1736094 1 SNP_A- rs4233429 90811924 90.811924 0.25 BB BB AB BB AB AB BB BB BB BB 1711115 1 SNP_A- rs665484 91375951 91.375951 0.512 AB AB AA AA AA AA AA AA BB BB 1714794 1 SNP_A- rs490800 92304926 92.304926 0.369 BB BB AB BB AB AB AB AB BB AB 1675488 1 SNP_A- rs6703310 93500761 93.500761 0.393 AB AB AB AA AB AB BB BB BB BB 1656572 1 SNP_A- rs223237 96276742 96.276742 0.476 BB BB BB BB BB BB AA AA AA AA 1755223 1 SNP_A- rs1911500 98291841 98.291841 0.738 AA AA AA AA AA AA AB AB AA AB 1691383 1 SNP_A- rs1838587 101983453 101.983453 0.525 AA AA AB AA AB AB AB AB AA AB 1725993 1 SNP_A- rs7521799 102944538 102.944538 0.619 BB BB AB AA AB AB AA AB BB BB 1689489 1 SNP_A- rs1576516 104210964 104.210964 0.452 AB AB AA AA AA AA BB BB AA AA 1684273 1 SNP_A- rs1919894 107240697 107.240697 0.381 BB BB BB BB BB BB AA AB BB BB 1733369 1 SNP_A- rs10494081 108114145 108.114145 0.667 AA AA AA AA AA AA AA AB BB AB 1715038 1 SNP_A- rs2026485 108978565 108.978565 0.333 BB BB AB BB AB AB BB BB BB AB 1699288 1 SNP_A- rs6682717 110527665 110.527665 0.441 AA AA AB BB AB AB AA AB AA AA 1750726 1 SNP_A- rs694180 111438255 111.438255 0.464 AB AB BB BB BB BB BB BB AA AB 1648811 1 SNP_A- rs1936061 112187978 112.187978 0.595 AA AA AA AA AA AA BB AB BB BB 1753842 1 SNP_A- rs2359417 113685242 113.685242 0.452 BB BB BB BB BB BB AA AB BB BB 1689065 1 SNP_A- rs3767824 118152606 118.152606 0.429 BB BB BB BB BB BB BB BB BB BB 1746401 1 SNP_A- rs1766803 119095860 119.09586 0.366 BB AB BB BB BB BB BB BB BB BB 1688653 1 SNP_A- rs477992 119969618 119.969618 0.286 AA AB BB BB BB AB BB BB BB AB 1708513 1 SNP_A- rs10494240 143040559 143.040559 0.321 AB AB AA AA AA AA BB AB AA AB 1701244 1 SNP_A- rs10494267 148366991 148.366991 0.321 BB BB BB BB BB BB AB AB BB BB 1706430 1 SNP_A- rs2879490 149760236 149.760236 0.381 BB BB BB BB BB AB AA AA AA AA 1680305 1 SNP_A- rs10494303 150706096 150.706096 0.571 BB BB AA AA AA AB AB AB AA AA 1723421 1 SNP_A- rs884664 151516798 151.516798 0.702 AA AA AA AA AA AB AA AA AA AA 1681003 1 SNP_A- rs10494315 154072954 154.072954 0.655 AB AB AA AA AA AB BB BB BB AB 1667931 1 SNP_A- rs919477 155585918 155.585918 0.25 BB BB BB BB BB BB BB BB BB AB 1647211 1 SNP_A- rs1149392 157241261 157.241261 0.286 BB BB BB BB BB BB BB BB BB BB 1662451 1 SNP_A- rs6683968 158923070 158.92307 0.571 AA AA BB BB BB BB AA AA AA AA 1695012 1 SNP_A- rs869513 159832184 159.832184 0.607 AA AA AA AA AA AA AA AA AA AA 1716490 1 SNP_A- rs4656422 161688624 161.688624 0.25 AB AB AA AA AB AB BB BB BB BB 1727494 1 SNP_A- rs4657482 162563307 162.563307 0.405 AB AB BB BB BB BB AB AB BB BB 1646555 1 SNP_A- rs2093658 164086850 164.08685 0.317 AA AA AA AA AB AB AA AA AA AA 1743854 1 SNP_A- rs1358948 165590931 165.590931 0.31 BB BB BB BB BB BB AB AB AA AB 1681011 1 SNP_A- rs2205848 166407951 166.407951 0.31 BB BB BB BB BB BB BB BB BB AB 1751990 1 SNP_A- rs10494487 167046739 167.046739 0.298 AB AB BB BB BB BB BB BB BB BB 1736240 1 SNP_A- rs3753538 168481215 168.481215 0.691 AA AA AA AA AA AA AA AA BB AB 1674510 1 SNP_A- rs10489280 169204277 169.204277 0.488 AA AA BB BB BB BB AA AA BB BB 1719434 1 SNP_A- rs989423 171514180 171.51418 0.75 AA AA AA AA AA AA AA AA AA AA 1753950 1 SNP_A- rs1359587 172487558 172.487558 0.691 AB AB BB BB AB AB AB AB AA AB 1722081 1 SNP_A- rs2861746 173128066 173.128066 0.452 AB AB AA AA AA AA AB AB BB BB 1694706 1 SNP_A- rs2493119 175995013 175.995013 0.333 BB BB BB BB BB BB BB BB AA AB 1733825 1 SNP_A- rs1281294 178629596 178.629596 0.714 AA AA AA AA AA AA AA AA AA AA 1671505 1 SNP_A- rs2274984 179839103 179.839103 0.524 AB AB AB BB AB AB AA AA BB BB 1694118 1 SNP_A- rs1184639 180355276 180.355276 0.357 BB BB BB BB BB BB BB BB BB AB 1644471 1 SNP_A- rs2840274 180942462 180.942462 0.429 AA AA BB BB BB BB AA AB BB BB 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1653419 14 SNP_A- rs10483573 46932227 46.932227 0.357 BB BB AA AA AA AA AA AA AB AB 1663303 14 SNP_A- rs698340 47611853 47.611853 0.585 AB AB AA AA AA AA AA AA BB BB 1664801 14 SNP_A- rs7146291 48172131 48.172131 0.274 BB BB BB BB BB BB BB BB AB AB 1722201 14 SNP_A- rs8006972 48690753 48.690753 0.31 BB BB AB AB AA AB AA AA AB AB 1650017 14 SNP_A- rs10498420 49483793 49.483793 0.476 AB AB AB AB BB AB AB AB BB BB 1720778 14 SNP_A- rs963626 50157439 50.157439 0.691 AA AA AA AA AA AA AB AB AA AA 1743320 14 SNP_A- rs1956574 51163026 51.163026 0.655 AA AA AA AA AA AA AA AA AB AB 1641756 14 SNP_A- rs7151306 52273870 52.27387 0.607 AB AB BB BB BB BB AA AA AB AB 1669704 14 SNP_A- rs877018 52892776 52.892776 0.451 BB BB AB AB AA AB AB AB AB AB 1748272 14 SNP_A- rs1382978 55788938 55.788938 0.536 AA AA BB BB BB BB AA AB AA AA 1714357 14 SNP_A- rs10483679 56503799 56.503799 0.61 BB AB AB AB AA AB AA AA AB AB 1714205 14 SNP_A- rs238376 57129665 57.129665 0.357 AA AB BB BB BB BB AA AB AB AB 1654106 14 SNP_A- rs10498488 58658876 58.658876 0.451 BB BB AB AB BB AB AA AA AA AA 1690578 14 SNP_A- rs9323353 59240800 59.2408 0.619 AA AA AB AB AA AB AA AA AA AA 1690058 14 SNP_A- rs2296274 60986931 60.986931 0.75 BB AB AA AA AA AA AA AA AB AB 1671347 14 SNP_A- rs9285590 61521469 61.521469 0.417 AA AA AA AA AA AA BB AB BB BB 1755551 14 SNP_A- rs1271582 64634456 64.634456 0.441 BB BB AA AA AA AA BB BB BB BB 1707294 14 SNP_A- rs10483805 67325404 67.325404 0.329 BB AB AB AB BB AB BB BB AB AB 1648725 14 SNP_A- rs1956528 67858721 67.858721 0.631 BB BB AA AA AA AA BB AB AB AB 1699466 14 SNP_A- rs749397 69414068 69.414068 0.262 BB BB AA AA AA AA BB BB BB BB 1682431 14 SNP_A- rs2215132 71545542 71.545542 0.262 AA AB BB BB BB BB AA AA AB AB 1674164 14 SNP_A- rs2803971 72182227 72.182227 0.713 AA AA AA AA AA AA AA AA AB AB 1672631 14 SNP_A- rs1028258 75447775 75.447775 0.726 AA AA AB AB BB AB AA AA AA AA 1648423 14 SNP_A- rs7152153 76265708 76.265708 0.286 BB BB BB BB BB BB AA AA BB BB 1700204 14 SNP_A- rs7156671 76991628 76.991628 0.7 AA AA AB AB BB AB AA AA BB BB 1701478 14 SNP_A- rs10483905 78043978 78.043978 0.429 BB BB AA AA AA AA BB BB BB BB 1706776 14 SNP_A- rs997842 78614233 78.614233 0.679 AA AA AA AA AA AA AA AB AB AB 1667157 14 SNP_A- rs2049826 79383063 79.383063 0.345 BB BB BB BB BB BB BB BB BB BB 1722889 14 SNP_A- rs2372083 81860288 81.860288 0.452 AB AB AA AA AA AA BB AB AB AB 1645339 14 SNP_A- rs2372424 83017248 83.017248 0.438 AA AA BB BB BB BB AA AA BB BB 1704748 14 SNP_A- rs8003423 83533541 83.533541 0.643 BB BB AB AB AA AB AA AA AA AA 1757272 14 SNP_A- rs1530325 84781909 84.781909 0.702 AB AB AA AA AA AA AA AB AB AB 1644835 14 SNP_A- rs10498604 86238836 86.238836 0.298 BB BB BB BB BB BB BB BB AB AB 1680733 14 SNP_A- rs8018273 86867956 86.867956 0.524 AA AA BB BB BB BB AA AA AA AA 1702796 14 SNP_A- rs429923 87481126 87.481126 0.405 BB BB AA AA AA AA AA AA BB BB 1687761 14 SNP_A- rs1742083 90256423 90.256423 0.321 AB AB AB AB AB AB AB AB AB AB 1725723 14 SNP_A- rs10498627 91041872 91.041872 0.583 AA AA BB BB BB BB AA AA AB AB 1661389 14 SNP_A- rs2148567 93244403 93.244403 0.286 BB BB BB BB BB BB AA AA BB BB 1705392 14 SNP_A- rs1456988 97557760 97.55776 0.679 AB AB AA AA AA AA AA AA BB BB 1734665 14 SNP_A- rs200331 98457298 98.457298 0.488 AB AB AA AA AA AA AB AB AA AA 1684765 14 SNP_A- rs3918051 99023837 99.023837 0.61 BB AB AA AA AA AA AB AB AA AA 1682935 14 SNP_A- rs10484072 102695759 102.695759 0.631 AA AA AB AB AB AB BB BB AB AB 1734911 14 SNP_A- rs1048257 104475429 104.475429 0.667 AA AA AB AB AB AB BB BB AB AB 1659209 15 SNP_A- rs1405186 21306806 21.306806 0.441 BB AB BB BB BB BB BB BB BB BB 1669336 15 SNP_A- rs2169637 25517776 25.517776 0.262 BB BB AA AA AA AA BB BB BB BB 1690082 15 SNP_A- rs10519635 27330404 27.330404 0.607 BB BB AB AB AB AB BB AB BB AB 1643639 15 SNP_A- rs4779462 28026287 28.026287 0.598 BB BB AB AB AB AB AA AA AA AA 1740804 15 SNP_A- rs2219507 29646927 29.646927 0.691 AA AA AA AA AA AA BB AB AA AA 1722463 15 SNP_A- rs10519737 30756749 30.756749 0.381 BB BB BB BB BB BB BB BB BB BB 1730684 15 SNP_A- rs1343900 31431890 31.43189 0.667 AA AA AB AB AB AB AA AB BB BB 1648795 15 SNP_A- rs10519956 32849133 32.849133 0.345 AB AB BB BB BB BB BB BB AA AB 1755583 15 SNP_A- rs1948650 33827340 33.82734 0.738 AA AA AA AA AA AA AB AB AA AB 1699406 15 SNP_A- rs10518868 34381353 34.381353 0.655 AA AA AB AB AB AB AB AB AA AA 1645977 15 SNP_A- rs471122 41345866 41.345866 0.3 AA AA BB BB BB BB BB BB AA AB 1665819 15 SNP_A- rs10519044 44169166 44.169166 0.381 BB BB AB AB AB AB BB BB BB BB 1673073 15 SNP_A- rs493728 48678247 48.678247 0.441 BB BB BB BB BB BB BB BB BB BB 1740676 15 SNP_A- rs1478200 51948279 51.948279 0.357 BB AB BB BB BB BB AB AB BB BB 1709940 15 SNP_A- rs2553222 52657040 52.65704 0.691 BB BB AA AA AA AA AB AB AA AB 1720532 15 SNP_A- rs4534776 55408068 55.408068 0.463 AA AA AB AB AB AB BB BB BB AB 1654466 15 SNP_A- rs1550574 56000660 56.00066 0.536 AA AA BB BB BB BB AA AA AA AB 1752856 15 SNP_A- rs2033721 58609267 58.609267 0.714 AA AB AB AB AB AB AA AA AA AB 1735597 15 SNP_A- rs3935962 59611593 59.611593 0.536 AA AB AA AA AA AA AA AA AA AB 1642536 15 SNP_A- rs10519148 60507655 60.507655 0.25 BB BB BB BB BB BB BB BB BB BB 1726387 15 SNP_A- rs2652824 61207054 61.207054 0.286 BB BB BB BB BB BB BB BB BB BB 1750348 15 SNP_A- rs10518707 65152676 65.152676 0.488 AA AB AB AB AB AB AA AA AA AA 1741266 15 SNP_A- rs305002 67928959 67.928959 0.595 AA AA AA AA AA AA BB BB BB BB 1739192 15 SNP_A- rs2128112 69973340 69.97334 0.262 BB BB BB BB BB BB BB BB BB BB 1677047 15 SNP_A- rs3898352 74308825 74.308825 0.631 BB AB AB AB AA AB BB BB AA AA 1698770 15 SNP_A- rs1446312 75199244 75.199244 0.738 AA AA AA AA AA AA AB AB AA AB 1654378 15 SNP_A- rs7163689 76352533 76.352533 0.488 AA AB AB AB AA AB AB AB BB BB 1657306 15 SNP_A- rs1001460 77291934 77.291934 0.56 AA AA AB AB BB AB AB AB AA AB 1701268 15 SNP_A- rs1320323 79128502 79.128502 0.59 AA AA AA AA AA AA AA AA AA AA 1689635 15 SNP_A- rs1846911 80255705 80.255705 0.329 AA AA BB BB BB BB AB AB BB BB 1749864 15 SNP_A- rs10520585 83462510 83.46251 0.286 BB AB AB AB AA AB BB BB BB AB 1714319 15 SNP_A- rs1961601 84030610 84.03061 0.31 BB BB AB AB AA AB BB BB BB AB 1654264 15 SNP_A- rs1122907 84708371 84.708371 0.691 AA AA AB AB BB AB AA AA AA AA 1650691 15 SNP_A- rs10520655 85887415 85.887415 0.595 BB AB AA AA AA AA AA AA AA AB 1665669 15 SNP_A- rs3817428 87216251 87.216251 0.75 AA AA AA AA AA AA AB AB AA AA 1694944 15 SNP_A- rs1079537 89675287 89.675287 0.452 AB AB AB AB AA AB BB BB BB BB 1683397 15 SNP_A- rs10520710 90688998 90.688998 0.287 BB BB BB BB BB BB BB AB BB AB 1752072 15 SNP_A- rs1989269 91611056 91.611056 0.305 BB BB BB BB BB BB BB BB BB BB 1731798 15 SNP_A- rs10520754 92760413 92.760413 0.548 AA AA AA AA AA AA AA AA AA AA 1728656 15 SNP_A- rs4321143 93957372 93.957372 0.262 BB BB BB BB BB BB BB BB BB BB 1700188 15 SNP_A- rs1551466 99344619 99.344619 0.345 AB AB AB AB AB AB BB BB AB AB 1686439 15 SNP_A- rs352716 100155950 100.15595 0.31 AA AA BB BB BB BB BB AB AA AA 1647533

In prior research, parthenogenetic activation of mouse oocytes has resulted in homozygous embryonic stem cell lines (Lin et al., Stem Cells (2003) 21:152). In human oocytes, the suppression of the second meiotic division after oocyte parthenogenetic activation and the generation of diploid embryos does not lead to the derivation of wholly homozygous hES cells.

Based on the HLA-typing results, differentiated cells derived from all phESC lines should be wholly histocompatible with the oocyte donors, making this a method to create cells of therapeutic use (Table 19).

TABLE 19 HLA-Typing for phESC Cell Lines MHC I MHC II HLA-A HLA-B HLA-C DRB1 DQB1 DQA1 phESC-1 A*01 B*15(63) Cw*04 DRB1*12 DQB1*06 DQA1*01 A*02 B*35 Cw*0708 DRB1*13 DQB1*03 DQA1*0505 phESC-1 A*01 B*15(63) Cw*04 DRB1*12 DQB1*06 DQA1*01 donor A*02 B*35 Cw*0708 DRB1*13 DQB1*03 DQA1*0505 phESC-3, 4, 5 A*02 B*52 Cw*03 DRB1*01 DQB1*05 DQA1*0101 A*03 B*22 Cw*04 DRB1*03 DQB1*02 DQA1*05 phESC-3, 4, 5 A*02 B*52 Cw*03 DRB1*01 DQB1*05 DQA1*0101 donor A*03 B*22 Cw*04 DRB1*03 DQB1*02 DQA1*05 phESC-6 A*02 B*07 Cw*04 DRB1*04 DQB1*06 DQA1*01 A*03 B*27 Cw*07 DRB1*15 DQB1*03 DQA1*03 phESC-6 A*02 B*07 Cw*04 DRB1*04 DQB1*06 DQA1*01 donor A*03 B*27 Cw*07 DRB1*15 DQB1*03 DQA1*03 phESC-7 A*01 B*38 Cw*06 DRB1*13 DQB1*06 DQA1*0106 A*02 B*57 Cw*12 DRB1*14 DQB1*06 DQA1*0103 phESC-7 A*01 B*38 Cw*06 DRB1*13 DQB1*06 DQA1*0106 donor A*02 B*57 Cw*12 DRB1*14 DQB1*06 DQA1*0103 NSF A*25 B*15(62) Cw*12 DRB1*04 DQB1*06 DQA1*01 A*32 B*18 Cw*12 DRB1*15 DQB1*03 DQA1*03

DNA-profiling of the genetic material derived from the human fibroblasts used as feeder cells revealed no contamination of the phESC cell lines with material from the human fibroblasts (Table 19).

The phESC-1 line remained undifferentiated during ten months of culture, spanning 35 passages. The other cell lines were successfully cultivated over at least 21 passages. The cells from all phESC lines formed cystic embryoid bodies in suspension culture and gave rise to derivatives of all three germ layers: ectoderm, mesoderm, and endoderm, after differentiation in vitro (FIG. 4). Approximately 5% of embryoid bodies from the phESC-1 line gave rise to beating cells five days following plating. The phESC-6 line produced pigmented epithelial-like cells (FIG. 41, K). Ectoderm differentiation is presented by positive immunocytochemical staining for neuron specific markers neurofiliment 68 (FIG. 4A), NCAM (FIG. 4B), beta III-tubulin (FIG. 4C) and the glial cell marker GFAP (FIG. 4D, M). Differentiated cells were positive for mesoderm markers including alpha-actinin (FIG. 4G) and desmin (FIG. 4J), which are muscle specific markers, and the endothelial markers PECAM-1 (FIG. 4E) and VE-Cadherin (FIG. 4F). Endoderm differentiation is presented by positive staining of differentiated derivatives for alpha-fetoprotein. These data demonstrate that phESC can be differentiated into the three germ layers that lead to all cell types of a human body.

The altered karyotype of phESC-7 may be a reason to exclude it form clinical use. Alterations of genomic imprinting in human embryos can contribute to the development of disorders linked to maternally or paternally expressed genes (Gabriel et al., Proc Natl Acad Sci USA (1998) 95:14857). In order to investigate other characteristics of the phESC lines, and to determine their suitability for use in cell therapy, imprinting analysis was performed.

Northern blots were made and screened with DNA probes SNRPN, Peg1_2, Peg1_A, H19, and GAPDH (as an internal control) as outlined above. Blotted nucleic acids were obtained from NSF, neonatal skin fibroblasts; hES, human embryonic stem cell line derived from fertilized oocytes; 1, phESC-1; 2, phESC-3, 3, phESC-4, 4, phESC-5; 5, phESC-6; 6 phESC-7. NSF RT−, hES RT−, 1 RT− are negative controls. FIG. 3 shows the results of the imprinting blot.

The maternal imprinting gene, Peg1_A shows strong binding in all of the cell lines tested. Weaker (relative to Peg1_A), but consistent binding was observed in all of the cell lines for the maternal imprinting gene H19. SNRPN shows binding predominantly in NSF, hES, phESC-4, and phESC-6. Peg1_2 shows binding predominantly in NSF, hES, phESC-1 (weaker signal), phESC-3, phESC-5, and phESC-6. GAPDH binding confirmed similar loading of RNA in all lanes.

Although the invention has been described with reference to the above examples, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the following claims.

REFERENCES

-   J. Cibelli et al., Methods for Making and Using Reprogrammed Human     Somatic Cell Nuclei and Autologous and Isogenic Human Stem Cells. US     Patent Application No. 20030232430, Dec. 18, 2003. -   H. Lin et al., Multilineage Potential of Homozygous Stem Cells     Derived from Metaphase II Oocytes. Stem Cells (2003) 21:153-161. -   K. E. Vrana et al., Nonhuman Primate Parthenogenetic Stem Cells.     PNAS (2003) 100 (Sunni 1):11911-11916. -   J. P. M. Dumoulin et al., Effect of Oxygen Concentration on Human in     vitro Fertilization and Embryo Culture. Human Reproduction. (1999)     14(2):465-469. -   B. Fischer and B. D. Bavister, Oxygen Tension in the Oviduct and     Uterus of Rhesus Monkeys, Hamsters and Rabbits. J Reprod     Fertil (1993) 99:673-679. -   D. I. Kaufman and J. A. Mitchell, Intauterine Oxygen Tension during     Oestrous Cycle in the Hamster: Patterns of Change. Comp Biochem     Physiol Comp Physiol (1994) 107(4):673-678. -   F. D. Houghton et al., Oxygen Consumption and Energy Metabolism of     the Early Mouse Embryo. Mol Reprod Dev (1996) 44:476-485. -   A. Van Soom et al., Prevalence of Apoptosis and Inner Cell     Allocation in Bovine Embryos Cultured under Different Oxygen Tension     with or without Cysteine Addition. Theriogenology (2002)     57(5):1453-1465. 

What is claimed is:
 1. A differentiated cell derived from a stem cell obtained from a parthenogenetically activated oocyte from a human donor.
 2. The differentiated cell of claim 1, wherein the differentiated cell is histocompatible with the oocyte donor.
 3. The differentiated cell of claim 1, wherein the differentiated cell is selected from the group consisting of a neuronal cell, cardiac cell, smooth muscle cell, striated muscle cell, endothelial cell, osteoblast, oligodendrocyte, hematopoietic cell, adipose cell, stromal cell, chondrocyte, astrocyte, dendritic cell, keratinocyte, pancreatic islet, lymphoid precursor cell, mast cell, mesodermal cell, and endodermal cell.
 4. The differentiated cell of claim 3, wherein the cell expresses neurofiliment 68, NCAM, beta III-tubulin, GFAP, or a combination thereof.
 5. The differentiated cell of claim 3, wherein the cell expresses alpha-actinin, desmin, or a combination thereof.
 6. The differentiated cell of claim 3, wherein the cell expresses PECAM-1, VE-Cadherin, or a combination thereof.
 7. The differentiated cell of claim 3, wherein the cell expresses alpha-fetoprotein.
 8. The differentiated cell of claim 3, wherein the cell comprises homoplasmic mitochondrial DNA (mtDNA). 